For me (as a builder), the biggest problem with Towny wasn't the towns or the features. It was the people using it. Anytime someone showed up who wasn't part of a town, there would be roughly thirty lines of "Join my town!" "No, mine!" "No, that town is teh suxxorz!" and so forth, even after the new player declined repeatedly.
It was the worst kind of spam I'd ever seen (I call it "townspam"), even more loathsome than gibberish. Now, I realize I'm just a builder, but I personally can't support any replacement for Towny that enables and encourages the same kind of behavior.