I've always hated when people spell words with numbers, so I'd lose Buffy's "Buffy + Angel 4ever" folder. *shudder* (And yes, I do text in complete sentences with capitalization and punctuation.)
I don't think there's necessarily anything wrong with the existing Buffy/Angel scenes in S1, but I'd have liked more gaps filled in. When did Buffy tell Angel her name (or find out he already knew it)? Was there actual closure to the Owen/Buffy/Angel stuff, not merely pretending Owen never happened? When was the moment Angel acknowledged to himself that he had gone from merely empathizing with Buffy and wanting to help her to being in love with her? A brief Buffy/Angel scene in "Witch" and "The Pack" each, and an extra one at the end of "Never Kill a Boy on the First Date" could've smoothed the way for the sudden intensity in "Angel." His absence for most of the rest of the season makes more sense in context, but I'd never say no to even more Buffy/Angel scenes.
I'm not a huge fan of the unnecessary drama between them at the beginning of S2 either. It works in "When She Was Bad," but it didn't need to extend beyond that. How did it take until "Reptile Boy" for Buffy to even discuss coffee with him? He was clearly done with being aloof from the moment he found her dead in that pool in "Prophecy Girl," and yet he goes right back to waffling and mostly only interacting with her when he has information for her. From "Halloween" on out, it's great, though.
More sparring matches. They're basically the equivalent of dance scenes in shows with lots of fights, and I never get tired of them.
For S3, it's not so much a Buffy/Angel specific issue, but I don't understand at all why Buffy couldn't just tell the Scoobies (or at the very least, Willow) that Angel had come back. Why was she isolating herself? Why were they so ludicrously unsympathetic? They all understood the difference between Angel and Angelus and should've known Buffy would never knowingly do anything to unleash Angelus again. This particular problem (the "gang up on Buffy whenever her balance on that pedestal they've stuck her on falters" problem) began with "Dead Man's Party," but its effects are pretty far-reaching. Maybe it makes sense for Buffy to keep Angel a secret while he's still all beast-like, but as soon as his mind is back, why keep hiding for three more episodes? And most of all, WHY did nobody ever research ways for making Angel's soul permanent? Not because it would've removed an obstacle between him and Buffy, but because it would prevent Angelus from ever coming back. All I want is for them to have at least raised the subject, even if they found out it was impossible to do it.
A more Buffy/Angel-specific issue from S3 is that the waffling about whether they're dating like the beginning of S2 is back, now with even more melodrama! It doesn't bother me a lot (I mean, none of this stuff really does, or else I wouldn't have been able to ship them so fiercely for the ~12 years I've been a fan of the show), but there probably could've been a less melodramatic way for them to have relationship struggles throughout the season than constantly breaking up and getting back together. Like if they'd had more conversations like in "Earshot," "Helpless," and "Gingerbread."
From S3 on—well, specifically after the network change—, more crossovers. I like what I've imagined for the off-screen rendez-vous after he found out she was alive again in S6/S3, but I would've liked actually seeing it even better.
Most of these complaints I direct more at the writing and other out-of-universe concerns than at the characters themselves. I think many of these issues were because there's "supposed" to be a certain level of drama and they couldn't necessarily get David for extra episodes in S1 or get around the network issues for the later seasons and stuff. I do, however, have a couple of character complaints. Buffy has a bad habit of making terrible assumptions and stewing over them before she has all the information ("Lie to Me" and "Enemies" jump to mind), and she also lashes out when she's hurt, seemingly in an effort to make sure Angel's hurting just as much ("Graduation Day," IWRY a bit, and "Sanctuary" a lot). Angel's too prone to accepting blame to really call her out on that (at least, when it's in his own behalf—he'll readily call her out on her unreasonableness if it's directed at someone else, like Joyce in "Ted" and Faith in "Sanctuary"), but I wish other characters had done so a bit more, particularly over the lashing out tendency.
Fortunately I've never been able to see the comics as canon on the same level as the show, so I don't have to deal with what I wish was different with Buffy/Angel there (which would be basically everything). Maybe if Rebecca Isaacs had been the artist from the start, it would've clicked as canon in my head, but (leaving aside the story and characterization and everything else I didn't like about the comics for a moment) Georges Jeanty's style rubbed me the wrong way immediately, so that never happened, and by the time Isaacs came on board, it was too late for that. I tend to view the comics as a whole as being the endorsed post-TV series timeline, but not the only possibility for where things could've gone next.
But yeah, at some point post-NFA, I'd want Angel to get the Shanshu and for human Angel and cookies Buffy to live happily ever after with Claddagh wedding rings, babies, a mixed martial arts studio that's only partially a front for training newbie Slayers, and growing old together.