That's definitely on my Lemmy wishlist -- some way to create merged communities. As it is now, there's too much potential for fragmentation across instances.
As of now, I just subscribe to whichever instance's community is the most active / has the most subscribers, which feels sub-optimal.
Same problem as with any social network migration: the network effect.
Sometimes the largest equivalent Lemmy community for a subreddit is tiny, or worse, nonexistent. Sure, you can go create one, but unless you can also convince other people to join with you, it won't be much fun.