I think I've played every version of this map on the TF2maps server and it's a refreshingly unique map amongst all of the Viaduct clones I see there. The gameplay is still annoying in some places, but you seem implementing the feedback well and I look forward to seeing it continue to develop!
Also, with the water features you've added and the pillars at spawn, I'm curious what kind of art style you were going to go for once the layout is finished.
Also I would suggest experimenting with a func_conveyor brush placed under the water set not to render. This would give the illusion of a sleight current (not sure how it interacts with water though thus the experiment). You could also try a trigger_push but that would be more difficult to set up right with such shallow water. Note I've used func_conveyor for some conveyors in my map and had to use a no_build brush over it because objects built on it stay still normally.
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