Unfortunately, although the lesser known games are often a lot more unique and interesting, they don't really have a community built around them. Yes, the reason is that they lack the balance necessary for really serious high level play. Building in that kind of balance generally requires a lot of game revisions and the financial success to finance extensive dev time just for tweaking.
For many years I never liked Street Fighter as much as other fighters because it seemed generic and bland and comparison, but I kept coming back because there were always real people to play with. Once I really got into it I found that there are levels of depth that you can't see at first, but ultimately make it very interesting.
I don't think the lack of balance makes these other games crap, they're just different. You can't take them as seriously but they're a very fun diversion.
Blazblue, is a nice exception. It's very unique, all the characters are extremely distinctive, and yet it's well balanced. Well some people will argue about the balance, but even though it's a fairly new series, Arc System Works built on their knowledge from Guilty Gear. It has a community now in part because of recent arcade releases.