I think it's perfectly fine as it is. I wouldn't want to imagine putting the extra effort of performing a death from above if I need precise timing when to press the takedown button while falling. Unless if I want to play Mirror's Edge, of course. I also wouldn't want to imagine falling to my death so many times if you don't automatically grab the ledge like what is seen in older FPS games. Climbing without using your arms and only with your legs is just not realistic. As for swimming, I recommend going to photo mode and see if it is knee deep or waist deep. I never had a problem with that either but a little perception added to the description would help out point out the problem.
I felt like the Death From Above (DFA) in FC5 worked better than in any of the previous games and very rarely if ever had issues with it, that said I have long been an advocate of initiating DFA with an additional button press if only because it would allow for more options in allowing us to determine intent to perform a takedown or simply land near an enemy. Never really encountered a situation like your water issue though, but seems more of a user error than the game's fault to be honest. In general I'd like to see significant improvements to the game's navigational capabilities. They don't need to get to Dying Light levels of mobility, but they could certainly use some more fluidity and fast, snappy movement in the game, though I can't say I want a ton of additional inputs to do it, the auto climbing works fine, additional inputs to grab a ledge is just excessive...