I don't have a MiSTer, but from what I've seen there are two things putting me off...
1) The frontend. Don't get me wrong, I don't want a flashy frontend. I've always hated the likes of hyperspin etc. Total overkill imho. But I would be planning on using the MiSTer on an arcade cab in my game room, which is regularly used by friends and family. It looks to me that it's fairly easy to get into the system menus and mess around with stuff. If it were to be viable in my game room I'd need a menu that just had a list of games, and a button to start a game, and exit a game, and *that's it*. I'd want absolutely zero way the kids can get into to a menu they shouldn't and mess something up. Admittedly I've not tried one, but from the videos I've seen I'm yet to be convinced this is possible? Somebody please correct me if I'm wrong!
2) Having limited space, I'd really like to use the MiSTer in a vertical cab for some classics... but I'd end up missing out on a few of my loved classics where cores don't yet exist. As I don't want (or have the space for) 2 cabs for vertical classics, I'm not sure that's a compromise I'd be willing to take, especially as a groovymame/CRT/high-framedelay setup solves the problem and is so good/authentic these days.
I love the idea of the MiSTer project, but I can't see myself personally investing in it at the current point in time for the above reasons.