I don't feel I had to specialize at all, quite the contrary, midway through the game I was an unstoppable killer and could manipulate the environment completely and reach all areas. it's true that you won't unlock every skill, but that's mostly because most skills are useless/boring, and that doesn't stop you from being a jack of all trades midway through the game. of course unless you deliberately limit yourself and makes human only and a typhon only run.
I dunno about other difficulties, I've just been playing on nightmare. I still don't think nightmare went far enough, either. Going back down to separate screen hacking after bioshock 2 is going to always be a big bummer to me, honestly. I can understand why they ditched real time inventory, even though dark souls has clearly shown it can work with a gamepad.
I also think the leveling system, as you pointed out, totally falls apart after a certain point in the game because you can just power level through everything. I think the hardcore mode they plan to do needs a hard level cap of probably 50 neuromods or so to really do the game justice. Once you can replicate neuromods the game essentially falls apart mechanically. This is a trend in basically every rpg these days (hilariously inverse difficulty curve, that is) though, so I can't be too hard on it.