Radar only actually shown what you could see personally (unless upgraded), the problem with animation takedowns was that they didn't allow other enemies to just up and shoot you, and yeah, I'm not a fan TPP cover systems, but I pretty much only used it to take screenies, so I forgot - I would stomach them if they didn't allow potshots/extra situational awareness with right camera positioning.
I played both HR and MD entirely without the cover system and would recommend that to everyone, but the lack of leaning is a major flaw. When sneaking you have to rely a lot on the radar to "see" through obstacles and around corners (which it totally allows you do without any upgrades whatsoever), and all in all it's pretty clear that they designed stealth around the cover system, i.e. the ability to sit behind a box and see the position of every single enemy in the room while remaining invisible to them. I guess one of the good things about playing in first person is that all of those stealth-related augmentations are at least potentially useful, since you have to use them instead of the TPP superpower. Still, ditch the radar and give me the damn lean buttons.
I think there are tons of problems with the ridiculous takedowns. For one, it's more satisfying to knock someone out with a baton than initiate a cutscene where your character beats someone up in a hilariously over-the-top fashion. The cutscenes also act as time-freezing spells, with everyone except Jensen and his victims being helplessly nailed to their spots, not just unable to shoot but unable to react in any way whatsoever until their buddies have been successfully beaten to a pulp. There's no risk of failure involved either. With DX's melee weapons (another thing that HR lacks) there at least was the possibility of screwing up if a guard happened to turn around at the wrong time (rare, I know), or you somehow didn't aim your strike properly and just pissed the enemy off instead of knocking him out. In HR it's button—awesome every single time.
Also, while I'm usually against gamist nonsense, DX's consumable lockpicks and multitools really did work well in terms of gameplay.