Nostalgia.
I tend to think that this is correct. BG2 was new and different and, to the best of my knowledge, really signaled the focus on NPCs and party interaction. It was new and fresh in those early days. Today, I think the main thing that has changed is my exposure to it. I've played Bioware's games, I know their tendencies, and have seen what they like to do with characters. Because I know their games so well I constantly remember back to BG2 and wonder why everything isn't as awesome.
Is Wynne any better realized than Jaheira? I really don't think so.
Nostalgia is part of it, but also the alchemy of gameplay, characters, story, exploration and... stuff was better aligned. Now it's predominantly emo-NPC romance-sex-look how great our utterly linear story is overkill with some twitchy combat BS bolted on. So, no, really, BG1 & 2 were better games.
It's the tyranny of plot, hack-wannabe novelists and cutscenes.