There are good and bad ways to seek church unity.
One bad way is is not to seek it at all, to give up on the project. I think that a lot of people who would say they are still working for unity have really embraced this option. We've been in the Age of Denominationalism (I put the beginning marker at about 1690) for so long that most of us have gotten used to it and don't really believe things could ever change fundamentally before the end of the world. We look around us and see all of the different churches with their myriad of sometimes large, sometimes extremely tiny but apparently non-negotiable differences, and we feel that the task is hopeless before, perhaps, the time of the millennium (when that will be being one of the differences). For example, is it really realistic to think the exclusive psalmodists and the hymn-singers will ever manage to come to an agreement? Really, no matter how much both sides might speak of being concerned with truth and being open to correction from the Bible, isn't everybody really just too biased and comfortable to ever expect any widespread change? Well, my answer is, I have no idea. Humans are humans, and they do tend to be extremely stubborn about such things. On the other hand, hopefully some of us are actually regenerate and really do care about truth to some degree, and perhaps we really could learn something new and admit that we are wrong if that turns out to be the case. Perhaps we could come to see ending the Age of Denominationalism as more important than holding on to some tradition that we really like and feel comfortable with but which really can't be defended biblically.
I truly believe that if we really wanted to, if we really cared, if we really put in the effort necessary, we could end the differences within Christianity on a widespread scale within a few months. The reason this hasn't happened, I believe, is ultimately because we aren't really trying. And perhaps we're not trying partly because we've convinced ourselves we can't do it. It's a self-fulfilling prophecy. We really need to snap out of it. Is the Bible clear, or at least sufficiently clear so that, with reasonable effort, we can understand what God is trying to teach us through it? Well then, we should be able to do this, shouldn't we? I think so. Instead of looking at denominational division as a permanent, unavoidable state of affairs we must live with, let's start looking at it as a temporary problem to be solved and which can be solved within a reasonable period of time, and then let's start acting accordingly and do what we need to do to solve it.
Of course, some other people are quite convinced denominationalism can be solved, but their method of going about solving it is unbiblical. I speak of those who would bring about the merging of denominations through a watering down of distictives due to apathy about those distinctives. Now, if our distinctives are not biblical, we should stop caring about them--indeed, we should reject them. But what I'm talking about is the downplaying of biblical distinctives, as if unity is the only real goal and who cares what that unity is really based in or if it requires us to abandon aspects of the whole counsel of God. This is unacceptable and unbiblical. We do not have license to compromise on anything God has taught or commanded us, no matter how comparatively minor it might seem (Luke 16:10, Matthew 5:18-19, Luke 11:42).
But if we're all going to insist on being completely biblical, and we're not going to connive at any systematic, constitutional departure from the whole counsel of God, doesn't that doom us to never being able to end denominationalism? How in the world could we ever get all Christians to agree on everything in the Bible?! Well, we probably won't ever manage that, even on the most optimistic appraisal. After all, not all professing Christians are real Christians, and even real Christians are still beset by sin. But, as I said above, I think that if we stop complaining about how impossible the task is and actually try to work at it as if it could be done, I think we would find it is much more doable than it may appear. It reminds me of junior high or high school students complaining about doing certain math problems (I ought to know, as I was certainly one of these!). "It's impossible!" they cry. "I'll never be able to do this!" Of course, if they stop complaining and work at it, before too long they'll find they can do it after all, and it doesn't end up being nearly as hopeless as it seemed at first. I think the same thing is true here. We just need to stop defeating ourselves before we even begin, and we need to patiently apply ourselves to the task until it is done.
But we do need a method. We need a plan for how we can go about efficiently dealing with our differences and trying to overcome them. So here's some thoughts on that:
Before my thoughts will be understandable, you need to understand my ideas on church unity, presbyterian church government, and the implications of denominational separation. If you aren't at all familiar with them, you can find those thoughts (among other places) here, here, and here. Actually, you really only need to read the first article, as the others merely expand on things mentioned there (as does this article).
So here's a systematic method for resolving denominational differences:
1. First of all, figure out which denomination you think is the right denomination to join. You're going to want to look at things from the perspective of that denomination. For me, it is the Free Presbyterian Church of Scotland (FPCS).
2. Once you know from which denomination you are viewing things, pick some other denomination. For example, I might pick the Free Church of Scotland (Continuing) (FCC). It would be good to first focus on denominations that are closest to our own positions, and then move out from there. I put forward the FCC because that may be the closest denomination to the FPCS.
3. Now, investigate that denomination, including probably talking to people and authorities in it. Ask them why they aren't joining your denomination. Ask them what is keeping them from doing so. Perhaps they will respond by simply saying, "Because I don't want to," but hopefully they will give you some substantial thoughts regarding why the two denominations are separate, and concerns they have about your denomination. I have phrased things the way I have--"Why aren't you joining my denomination?"--because my assumption is that you are part of the denomination you are part of for substantial reasons, because you believe it has a right to separate existence. If that is true, then it is appropriate for you to approach the other denomination with some confidence in your own position (though without behaving cockily, of course--and being willing to respond to their questions to you as well). Asking this sort of question will help produce a list of things that are keeping the denominations apart.
4. Next, go through the list you got from #3 and systematically discuss each issue, dialoguing to reach an agreement. Your list might include historical issues--such as, "I don't join your denomination because I think it came into being schismatically and needs to repent." In those cases, your dialogue will involve an examination of the historical issues with the goal of reaching agreement on them. For example, the FPCS and the FCC disagree about whether or not the FPCS should have left the earlier Free Church in 1893 or whether they should rather have remained seven years longer and come out with the group that became the modern Free Church. So my conversation with my FCC interlocutor will involve questions such as, "Was the 1893 FP split justified?" This is important, because if that split was justified, it is evident that the FP church has a higher historical claim to have a right to separate existence, since the modern Free Church came into separate existence after the FPs did. So if both denominations are exactly the same in every other way (which is not quite the case), the default goes to the FPs and the FCC ought to see its separate existence as schismatic. If I and my FCC correspondent could agree on this, the conversation would then be over.
Your list will likely include doctrinal issues as well. In these cases, of course what you will want to do is sit down and go through those issues one by one to see whose views are more biblical. For example, say you disagree about the celebration of extra-biblical holy days. Well then, the question will be, "Is it biblically justifiable for the church to incorporate such celebrations in its ongoing worship? Does this violate the regulative principle?" Each question you look at might raise other questions which also have to be looked at. Just keep at it systematically until you've gone through what needs to be gone through. The temptation will be to give up because it seems too hard, or to get frustrated with each other, or to pull out oneself if things get uncomfortable. Well, don't do those things. Keep at it with honesty and systematic-ness.
5. Once you've gone through everything and reached agreement on each point, the two of you (assuming a conversation of two here) will be ready to join in full communion. Either he will join with you, or you will join with him, or some other option, and you will agree on what needs to be done. If we will all follow this sort of pattern on our own, in conversation with friends and others in other denominations, in larger groups (but they must be strict about not getting off track in any way), etc., I believe that we will largely end denominationalism within a relatively short period of time. We won't fully end it, for undoubtedly there will always be those who simply won't be able to go along with where things lead for various reasons, but we will be far, far, more unified than we are now, and that unity will provide pressure for further unity and unification efforts, and it will strengthen the proper denomination and weaken the others. We may find that the schismatic denominations will quickly wither away once those who care about truth in the midst of them move off to a better denomination and they are left nearly only with those who don't really care about truth. They will probably liberalize at an accelerated rate and blow up before too long, and this too will aid church unity.
I think part of what holds back church unity is the sense that it should never have to involve any of us having to simply leave our current denominations. We imagine we should be able to stay where we are and just come together with other denominations. But unless every single person in all the schismatic denominations decides to abandon his wrong choice of denomination, this is not going to happen. If unity is to be sought, we all, as individuals (or smaller groups), must decide to do the right thing whether all of our denominational companions agree or not. If there are enough people who agree they should leave their denomination, perhaps they may have enough power to vote the denomination into an agreed merger with the proper denomination, but this will not always happen. I think we have a duty, when it is possible without shirking other duties, to leave schismatic denominations and to join the proper denomination, perhaps sometimes after a reasonable, limited time spent trying to convince others to join with us. A lack of willingness to consider that this course of action will be right and necessary sometimes will hinder unity.
So does all this sound naive? I understand. But I really don't think it is. Again, if we believe that God has been successful in communcating to us a Word that can be understood, and if we approach that Word and all the issues that cause division honestly and with full and proper care, we should be able to do this. With God's grace, I think we can, and we don't need to wait for the millennium (and without God's grace it will never happen to all eternity). Let's commit to doing our part to end the Age of Denominationalism within this century. The biggest, most difficult obstacle to overcome will not be any particular historical or doctrinal issue we may need to deal with. The biggest obstacle will be overcoming our own bad attitudes and committing ourselves truly to do our duty, putting it before our personal preferences and prejudices whatever forms they may take.