Tough decisions, here. I've always loved the idea of soulmates and I'm interested in things like Loveless because of it. At the same time, it seems really tricky to run a roleplay based that way because of the flakey nature of RPers (me included, I'm afraid). I did run a Legend of Mana site, which has a race called the Jumi which have a sort of soulmate bond thing going on and we just let people choose theirs. Of course, there was stuff in canon that stated they had to go through a sort of ritual in order to BE bonded, so it could be a thing that they chose to do. (And sometimes one would bond to somebody without realizing that their first and true bond was still alive!)

I think it's a tricky thing to do but I'm interested in seeing where it ends up going.

As for advice, my best advice is to make sure that whatever you DO decide to go with, try to make it "flake-proof" so that if people poof, the people left behind aren't stuck without any direction or having to delete/retcon everything that already happened (I know I hate doing that--so much wasted time and growth!) So yeah, maybe make it something they can establish with a new person if they need to and I think that might work.