I think getting rid of Clam Blitz would be a huge mistake. Imo it's the best mode from a viewer's perspective. Its only real problem is Kraken cheese, and arguably a dearth of great maps. Popgun said in a recent Popcast that if Kraken cheese is really that much of a problem we should just consider banning it instead of condemning the mode entirely, and I 100% agree.
As for Rainmaker/Tower Control, I think getting rid of them entirely would remove some interesting diversity from the game. That being said, I think we could make the argument for treating them a single mode instead of two, and make it so every three games is Splat Zones, Rainmaker/Tower Control, Clam Blitz. Personally if we're not going to do all modes equally I'd rather have this.
And I don't like Chara's suggestion for Zones every other map because I don't like the idea that a team would be able to win a set only by winning Zones. You should have to win at least one other mode imo.