Snake works as the type of map it is. It has a one dimensional mid and no flank (2 chokes that the combo can rotate between doesn't make the other one a true flank), but it kind of works after years of teams getting used to it. If you want to fix these problems you'd be better served making a brand new map, as it would require ripping out huge chunks and completely remaking them.
Don't pin the "kaidus hates snake" thing on me as that's not been the case for almost 2 years. I think this style of map is inferior to something like badlands, but snakewater does this style better than anything else and it's nice to have the variety. Fix any bugs and leave the core gameplay as it is.
Edit: One thing I wish was changed is the old dropdown room (that sticks out of the wall onto cp2 balc) that stops you from jumping from that area. It's annoying and I wouldn't mind seeing it pulled back into a flat wall.