I also prefer seperated skills for different weapons. It just results in a certain feel of accomplishment, training your longsword skill to an "elite" level, beyond your other weapon skills. It's yet another way of customising your character - which, along with exploration, is the main thing about CRPGs for me - and knowing that it's reflected in the stats is always way more gratifying than "pretending".
I agree that skills should be linked, ideally, there'd be a hierarchy of skills: Fighting - Slashing Weapons - Swords - Longsword. Some games have implemented similar systems, I think they make a lot of sense both in terms or game-internal realism and gameplay. Personally, I'd even go as far as accruing experience with one particular item, although it's probably a bad idea because it makes switching to a new found item so much harder.
Anyway, I agree with Creston in that I'll take a simplified CRPG over no CRPG any time. And actually I think that's true for most RPG fans. I will still bitch about it, though. And lockpicking minigames don't count as innovation for me, if anything they are a step in the wrong direction. My thief has a high lockpicking skill, I don't, so why make me jump through hoops.