Installer's still in beta, and although Cydia comes from much more mature roots (APT), they're both still very much in development. Just a month or two ago, under 1.1.x, Cydia was generally a disaster and Installer was pretty flawless. Cydia beat Installer out of the gate with 2.0, but who knows? Give them both time. We're not at a stable jailbreak installation mechanism just yet.
(FWIW, I installed Installer and not Cydia purely because there were limited reports in 2.0.1 of major iPhone slowdowns if Cydia was installed and the iPhone was restored from backup, but I haven't really installed jailbreaked apps in this round, and there isn't too much in Installer repositories right now).