I've used both tools for two start-ups now. I can't imagine using anything else (well, Redmine is a nice free tool). But you're not in the minority in startups. I personally can't understand how anyone is productive with PivotalTracker, Lighthouse, or GitHub Issues (at least the older one). But people are and to each his own.

FWIW, one of the reasons I love both of them is they're the only tools of their type that I've been able to throw a non-tech person at and they can use. When roping the spouses into helping out, that counts for a lot.