Not that I'm some huge Andrew apologist, but I think the nerd jokes can come off stale and just haven't aged as well because nerds have been brought into the mainstream with stuff like Big Bang Theory and the onslaught of nerd/gamer culture. The kind of stuff coming from Andrew wasn't necessarily ahead of it's time, but it is a lot less unique now or at least seems that way to me. I throw Big Bang Theory in there not because I've ever even watched it or have an opinion, but because I'm relatively nerdy compared to many people I have hung out with, and the non-nerd people thing BBT is the funniest thing ever, which I'm inclined to be skeptical about.
Jonathan might've been interesting, but I think it wouldn't have worked for me, primarily because of his history with the Scoobies, as strange as that sounds. Their first interaction with him was Buffy talking him down from suicide and then he just showed up occasionally until the end of high school. Then you have Superstar, where his self-centered narcissism caused all kinds of problems. On to the Trio, where he purposely started to screw stuff up for them and even tried to kill Buffy. Yeah, he was a misunderstood nerd, but that doesn't overshadow the fact that he was a wishy-washy, totally self-concerned jerk and attempted murderer. Plus, the whole time, no one really ever gave a crap about Jonathan anyway. Even when he showed up and wasn't trying to kill someone, they always just patted him on the head and sent him on his way.
Andrew, on the other hand, may have been stirring up all kinds of crap with the trio, but it was mostly just so he could belong with others, which I think shows itself in his interaction with the Buffy gang as well. And unlike Jonathan, who if captured would probably have sat in the corner quietly, Andrew actively attempts to be involved, regardless of whether they want him to or not. I'd rather he be there, possibly obnoxious but with his own small character stuff, than a non-entity who's there because the show didn't know what was left to do with him. And because The Trio was a group of humans and most of what they did was supernatural stuff, you can't simply hand them over to the police, especially in a place like Sunnydale. It makes sense for Andrew to be there given the previous events.
Also, comparing Andrew's nerd stuff to the one-liners, I'm pretty sure it was intentional that he's not as like-able or witty. He doesn't belong in the group, which is why he's there. And regarding him taking up space that other characters could be using for their character development, I think they give him enough time to work his stuff out without taking away too much of everyone else. I think Xander could've done with some more screen time, but the Season 6 finale put his character in a really good perspective with regard to him being almost the strong, silent-yet-witty backbone of the group, a far cry from bumbly, skateboarding pilot episode Xander. He gets a few really good moments in season 7 regardless, I think.
