I really don't see a problem with them fundamentally. Mostly they're just poorly balanced and there's too few of them. They give your character cool little perks is all. I'm not sure what kind of theme you're thinking of that wouldn't homogenize them. I actually found the NWN feats pretty boring to be honest because they mostly felt pretty samey. They're much more similar to Fallout Perks, which are almost exactly the same, a hodgepodge of benefits that don't really fit anywhere else.
I do think some talents, like Zombie or Pet Pal, are a bit weird to gain partway through the game without so much as a peep from anyone (well, Pet Pal does give you a lot of peeps from animals, but none of your party members are like, "holy crap, you're talking to a rat?!"), but most of them are okay. That's simply a limit of the writing/scripting. Maybe they'll make talents more significant for RP purposes in D:OS 2 (I do think they're interested in doing that.) Maybe even certain talents like Pet Pal could be earned through quests or other actions, like they do in Fallout, which makes for extremely satisfying quest rewards. But most can stay in a talent list fine. Maybe if they added a lot more, they would need to sort them in a different way, but there's not too many to go through for now.
I suppose, I guess. The perks in Fallout weren't exactly random, though, at least not in the same way it was in D:OS. The first Fallout had 53 perks, but only 3-4 were straight up damage and it was a very specific kind of damage (thrown weapons or hand-to-hand/melee i.e. the very unusual damage type for the setting). They also didn't have needless downsides to them. Some of them were really powerful, like Cult of Personality. Their unifying theme in this case would be "RP" and sometimes "Convenience", maybe even "non-combat" with a few exceptions. That's what I'm talking about.
The feats in D&D (and by extension NWN) didn't exist in a vacuum like in D:OS and Fallout. They were used to not only boost your power, but also unlock the prestige classes which were HUGE game changers. Yeah, you had the no-brainer ones like Weapon Specialization and Weapon Focus, but the root of D&D is in table top gaming and that is a bit different than a video game.
