I've never found myself wanting for a cover system. I've always found crouching or standing behind something solid to be perfectly sufficient, especially since you're able to lean from side to side, which means you can still pop out to fire off a few shots while exposing as little of yourself to enemy fire as possible.
I think the cover system in Human Revolution was more just replicating something you'd do anyways in the original. Hide behind cover. Until of course you have the 85% versus everything resistance. Plus, if I'm low on medpaks? It means its stealth time!
I'd like a lean system added on (my own idea for a vaguely related game concept includes the new Medal of Honor cover system and leaning outside of that), but the cover system tends to make things easier since you can see exactly what parts of your body are sticking out (an impossibility in first person orientation, as you don't have any sense of awareness of where any of your body parts are) and lets you blindfire. Human Revolution actually made the smart decision of having almost no accuracy during blindfiring (even in Gears of War is just serves as a "less accurate normal shooting"), but it does suit a more rapid combat style where you can respond to enemies in cover by running up, ducking behind the pile of boxes they're hiding behind, and blindly sticking a shotgun over and into their face when they pop up.
As for the training system: That's exactly how it should be. Deus Ex is designed around forcing the player to specialise and actually use their chosen skills to play the game. If you could easily overcome a poor training level with player skill, then what would be the point of any sort of levelling system in the first place? It's also why every new augmentation comes with two possible buffs, and you can only pick one, and why there aren't enough augment upgrades in the game to max out all of your augmentations. It forces you to pick and choose the augmentations that fit your playstyle. Then of course the highly limited inventory forces you to do the same with your equipment. In effect, it creates a completely organic class system. Add to that the level design which makes any halfway reasonable build perfectly viable and it just works. It's what makes Deus Ex a proper RPG/shooter hybrid rather than a shooter with token RPG elements.
Story was decent, but the gameplay was... too simple. It took away meaningful choice making with your augments.
First off, HR actually included the limited inventory and augmentation standard from the first game. Other than the choice of inventory expansions as an augmentation and making ammo take up space (the original had it off in the ether somewhere, untainted by the grid), the grid system is almost exactly the same in size as the original and actually restricts you MORE, since ammo has to be included as well as everything else. There's also only 21 Praxis Kits in game (it takes 68 points to fully upgrade) and it costs a total of 45,000 credits to purchase 9 of them, which only compulsive thieves who scour every area for cash will be able to easily acquire. So someone will likely never manage more than half of the possible upgrades at the most before completing the game even including XP on top of that, which fits into the "Choose carefully" bit.
On my second point, the training levels in the first game were downright ridiculous and completely destroyed suspension of disbelief: an augmented supersoldier and trained government agent can barely even hold a weapon steady enough to hit the target at 50 yards unless he decides to use those augments to increase his skills to the levels of an average USMC rifleman? Along with stretching believability even if you tried to justify it, it's immensely frustrating for players who have the skill to do the task (and could probably accomplish it themselves in real life) but are hamstrung by their character shooting like a drunk. Adam Jensen starts with the level of training and skill that someone in his position should rightfully have, and the augmentations do exactly that: augment his ability. He can use his Praxis points to steady his aim or reduce recoil, but he never needs to use them just to get himself past the competency level of your girlfriend trying out a shotgun for the first time out in the woods.
As for making augmentations "meaningful", HR always provides more than enough choices for people who took any augmentation to make it through. Someone who emphasized hacking and break through locked doors and computers faster (and has access to hacks that literally aren't possible for those with lower skill levels), someone who emphasized stealth can more easily sneak around the guards and cameras, someone who emphasized combat can shoot his way through, etc. Certain augmentations like the wall breaking and Icarus Landing System open up entirely new paths. But you're never going to be left thinking "Dammit, I should have chosen X augmentation beforehand." Because really, you can't expect the player to predict what may come in handy far in the future and players probably won't be happy if they spend the entire game focusing on one play style that works only to find that it's useless at a certain point. Even the last level's pseudo zombie apocalypse still incorporates elements of the available playstyles and even makes it possible (albeit extremely difficult) to make it through non-lethally, while still keeping it new and wild enough to force players to adapt or die.
As for regenerating health, it's really not suited to a game like Deus Ex. It works quite nicely in a more linear game, where there's little scope for searching for health pick ups, but in a game with very open levels like Deus Ex, they provide yet another rather compelling reason to explore. It also means doing badly in a fight has some consequences, which for an RPG is definitely something you want. Sure, you can get an augmentation that regenerates health, but it uses up bioelectricity like it's going out of fashion, which itself is a finite, non-regenerating resource. You could certainly argue that it's overpowered, but it's most definitely not the same thing as free, constantly regenerating health.
Regenerating health became popular for good reason: limited supplies. Both games are infamously lethal (even on the easiest difficulty, HR will kill you quickly if you get caught in the open for mere seconds), but forcing the player to rely on limited medical supplies very often resulted in the player being caught with too little health to make it through the next section, but no supplies available to revitalize them. It's extremely annoying, especially since both games make such useful items in general relatively uncommon and have limited inventory space to try and fit everything in. Making it through Deus Ex gets frankly annoying sometimes, because you die quickly (especially early on) and you may have absolutely zero chance of recovering any health if you manage to hide. It's all in the name of giving the player a fighting chance, which is kind of a necessity if you want your game to have more than niche appeal these days. It's why my own game concept follows the Dwarf Fortress or Nethack manifesto of extreme unfairness and forcing creative thinking, but also understands the game's niche and how it's not meant to really be made for mass consumption.
Also sounds like you got a broken version if it takes ten seconds for them to notice me. I had them able to see me pretty readily at a distance unless i was crouching in shadows. It uses an organic stealth system like Thief, it just lacks a proper light gem so it feels a little wonky.
I think you misquoted there.
I liked HR but my biggest problem was the end game
The endgame was almost exactly like the first one: you get several choices and you have to pick one. They were admittedly limited by the story being a prequel, but they explicitly made it so that there wouldn't be a bunch of non-canon endings: the progression to Deus Ex has elements that fit every possible ending, so any one of them could be correct.
and the fact there was no reason to use lethal strikes
You mean the melee strikes? They actually do serve an important purpose: unconscious enemies can be woken up if they get found. I decided to do a 100% non-lethal sneaking run through the police station recently, and I kept running into problems where the cops would quickly wake up whoever I knocked out (especially if I ever got caught, as they'd promptly start patrolling the area). I had to get around this by quickly knocking them out and dragging them into a nearby air vent until everyone on the floor was stuffed in a tangle of bodies blocking damn near the whole thing.
Also, the office floor is probably one of the hardest areas to stealth through. Along with being utterly loaded with cops (all of whom will promptly start shooting you simultaneously if they catch you uninvited), there's a lot of windows and open doorways that expose you as you walk by AND patrolling cops in the halls behind those windows. It takes impossible levels of speed and precision to stealthily make it in and out of the morgue unless you find an alternate route, and you'll probably end up throwing flashbangs and shooting tasers and PEPs while sprinting upstairs to escape through the vents.
Oh, and if you get caught, all cops outside become hostile. Yeah, all the guys patrolling in full body armor and carrying shotguns who call for backup if you fight them. You're basically left sneaking around Detroit for a long time.
