While I didn't mind them at all, many people seemed to have a problem with the fact that direct confrontations with Human Revolution's bosses were unavoidable and must be killed; the no kill achievement specifically mentions the bosses don't count. They also had large Hit Point pools, and only one of them had an environmental means to inflicting damage. So people complained that their characters at these stages built solely for stealth/non-lethal were not suited to gunfighting with bullet sponges. It is worth noting that all the bosses were still vulnerable to things like Gas, EMP, the stun gun, the typhoon and mines, just that they aren't incapacitated instantly. All the rooms include weapons, ammo and health. I certainly thought you were presented with plenty of options.
I haven't played the original, so I can't appreciate the significant differences with how it handled bosses. If I was to say anything negative it would be the boss characters are the least interesting characters in the whole game. So aside from brief glimpses of them during the prologue and a few of the cutscenes, the only one I cared about fighting was the one who beat up Adam at the end of the prologue.
They tried to address this in the final confrontation of The Missing Link DLC episode, with the final boss being subject to the same rules as normal enemies, only slightly stronger, and still vulnerable to takedowns and such, and as such could be beaten lethally or non-lethally. He was also built up to as being the major antagonist for the chapter as it built up to actually having to confront up before escaping. Instead, you had to fight or sneak full a large room full of enemies that are on alert for you to make it to where he was hiding.
On speaking of the speech augmentation, there are a couple of characters that are immune to the Influence option and call you out when you try to use it. I liked that. Also, I can remember a couple of examples where you needed it to influence the character into giving something up (whereas without it the options would not appear and you'd need to take a more... direct approach), but I'm sure it was only side missions .