With Rainmaker, I believe they should make it so while holding the Rainmaker, all your gear abilities and stuff like weapon weight are completely null. Meaning no matter what equipment you have or what weapon you were using, when using the Rainmaker, none of it counts. Your movement and swim speed are locked, stuff like kill abilities or respawn abilities are also null. Basically, the Rainmaker can't favor one person over another, its always equal.
Clam Blitz, in order to discourage super jump throwers, I think they should make it so when you super jump with a Super Clam, when landing, you'll have end lag where you can't do anything for about a whole second. I don't mind the ability to Super Jump to get close to the enemy basket, it allows for sneaky strategies, but the ability to super jump next to the basket and have it be a fairly safe way to score is another story.
All Special Weapons will cause you to drop your Power Clam upon use, no matter what Special. You can also not pick up a Super Clam while using a Special.
For Ranked rotation. I'm actually not completely on board with making all modes available at the same time. I'm not saying that I wouldn't like if it was that way, but the issue of would queue be full enough always comes to mind. As a slight compromise, why not have 2 Ranked Modes up at any time on queue? They have two different queues, but share the same maps. This applies to League as well. More than likely at least 1 of the modes in rotation would be something you would want to play.
Tower Control and Splat Zones, I already think are fine in principle.