I'm also very fond of Rainmaker. Always loved the freeform movement across the map that most other modes don't accomodate, the Rainmaker itself is a cool weapon and while not perfect, the checkpoints added in 3 make this the most balanced iteration yet. I think they add a lot, actually, since most maps have two checkpoints that force teams to make a decision on the fly.
Clam Blitz is also my least favorite mode, but it's less to do with the mode itself and moreso with how limited communication options are in-game. Clam Blitz really demands communication, and the pings we have really don't cut it - nevermind the fact that some people just don't know how to Super Jump. Playing in Series/X is somewhat manageable - playing in Open, where you might get matched against a full, coordinated team is a nightmare.