When you ask what the "best" mode is, then ask what the "most balanced" mode is, they're two completely different questions. I have a hard time supporting Rainmaker as balanced or even enjoyable when one sneaky Sanic build can plow through the side streets and cap the Rainmaker within the first 30 seconds (which I've done. Sorry not sorry.).
I legitimately suck at Zones for no apparent reason; my Zones game is B or B+ at best while I hover between A+ and S for Tower Control. Because I play blasters mainly, I find TC to be the best for my own comfort, playstyle, and enjoyment. That said, because it favors AoE damage so heavily I can't really justify TC as being balanced either.
In the end I suppose that all game modes are skewed in some way: Zones in favour of ink spreaders, TC in favour of blasters, and Rainmaker in favour of heavy mobility builds. Because of this, and the tremendously different playstyle and mindsets involved, I'd like to see separate ranks for each game mode in Splatoon 2. I'm not sure how they'd factor in general gameplay, but any ranking system is bound to be better than the floating ladder that they've got now.