A short while back, I was trying to get into Deus Ex: Human Revolution. For the most part, I was actually enjoying it. Some may not like the "pre-baked finishing moves" aspect, but I personally don't have too much of a problem with them as long as they're entertaining to watch and there's at least some variety to them. The nameless nature of your antagonists early on can be explained by the fact you're still trying to figure out who the hell they are, and they're certainly not going to flat-out tell you (apparently they didn't graduate from the Bond villain school of bad guys).
But the boss fights, ugh. Or more specifically, the first boss fight, UGH!
I'd been specializing in stealth and non-lethal takedowns whenever possible. With a tranq rifle and a tazer pistol, this was very possible, thankfully, but then came that first boss fight with the meat wall that just marches up to you and caves your head in at close range, and blows your ass in half with an arm-mounted machine gun at long range.
I didn't have a ton of high damage weapons on me, so I was trying to make do with stun grenades, sneaking around and capping at him from a distance with a revolver or trying to lure him into a land mine. Problem was, his tendency to be able to lock onto my position made me wonder what kind of augs he had (motion sensors maybe?).
It seems to me like this boss was really meant to be taken on directly by someone with augments designed for direct combat (like improved skin armor and the like) and armed with heavy ordinance. It didn't mesh with the augs I'd been going with so I was at a severe disadvantage. So I've wound up restarting the game from scratch, this time intending to go for a full lethal combat (but still stealthy) approach. But I don't like it that much; a character using lethal force when he has viable nonlethal means at his disposal seems a touch amoral and a bit bloodthirsty. I still try to use nonlethal takedowns when I can, but I don't carry a bunch of nonlethal weapons with me.
This wouldn't be such an issue with me if they didn't try to put some of the bad guys in a sympathetic light. Take the very first mission. We've got terrorists holding innocent factory personnel hostage and getting ready to set off a chemical bomb. Sounds like they're pretty much rotten to the core and deserve to get a bullet, right? But then their leader starts talking like some tragic hero who's been forced into the position he's in. And to get this guy to keep from getting his hostage killed, you have to talk him down by SYMPATHIZING with him. That smacks of insincerity to me, considering I've been gunning down his men whenever they've been in a position that isn't convenient for me to sneak up behind them and brain them with a metallic fist.
I guess it's to the game's credit for immersion when I start worrying how my in-game decisions reflect on my own moral leanings. Personally I don't have a problem with using lethal force for self-defense; when somebody's threatening you or an innocent person, you have to do what you have to do. Killing someone unsuspecting is much more questionable. In the aforementioned terrorist/hostage taker scenario, it's understandable because they're putting people in harms way. But later situations, like infiltrating gang territory, not quite so much because this time you're the aggressor.
The game puts you in so many different situations with different circumstances, no one approach is right for all of them. Sometimes it's alright to sneak in and start doing wetwork, while other times you have to be more of a cop and use lethal force only when there's no other alternative. The game shouldn't encourage specialization if it's going to toss you into situations that only have one viable solution, because you might not have chosen that particular specialization.