- Wario: if he was part of Mario, there would've been no reason not to include him (keeping in mind that during Melee, Mario was still way ahead of Pokemon, so "balance" then wouldn't matter); if he was considered his own series, then he just flat-out didn't want him in because Wario Land was doing great. Either way series performance didn't matter there.
I wouldn't say that there was no reason. Certainly a tthe time, the Wario series was doing great, and Wario was an established character ooutside of Mario, but for whatever reason, Sakurai didn't view his series as a seperate one like the Yoshi one, and Wario was lumped in with the Mario crowd. But when you view it like that, there should be even less reason why someone like Wario be cut right? You said it yourself, in that at the time Pokemon hadn't really caught up yet to total sales, and curent Mario games were still doing great. The problem as I see it, is that Sakurai simply put limits on how much one series could have. You yourself acknowledged that if every series had exact representation based around sales and sales only, then there would be a huge amount of Mario and Pokemon characters running about, and that'd be it. Its clear though that Sakurai puts limits on the popular series though to make sure they don't go out of control. The Mario series there had the largest amount of characters, and thus as Wario was still considered to be part of the Mario series, he got bumped off for later. (Dr. Mario, as said, was just an easy to add in clone. )
- Goroh: F-Zero did somewhere around Star Fox/FE territory (all of which were better than Mother) between 2001-2006. Also had more content than either series counting the anime. GX has outsold every FE to date except maybe FE3. So clearly it wasn't series performance.
Yes, F-Zero has the sales to warent an extra character, but it doesn't quite have the characters. If you go by sales alone, without paying any attention to the characters being added in, we'd at least have two or so different breeds of Nintendogs. F-Zero has more characters than most series, and they generally all have their own unique personality, but they still hide behind their cars for the majority of the games, and unlike the SF crew, aren't talkative. Thus, what you have to do is create an entire moveset from scratch and that seems to be a large, though not impossible to deal with, road block. Captain Falcon probably got through it due to the whole Ryuoh stuff, and I can easily see Goroh making it through next game (and BS probably would have done so in Brawl, if not for Ganny) but its still a lot of effort for something that should already be there in lesser selling series.
As for the anime though, there actually is content there that could be used for a fighting game, especially with Goroh. He actually did use his sword some times to do crazy stereotypical samurai stuff. Why the anime wasn't counted in any real way, I can't quite say, but if you really did want to take the anime into consideration, then you sort of have to push Goroh back a bit, since his role in it wasn't as large.
- Wolf vs. Dixie: DK has always done better than Star Fox in every regard. Calling her exclusion a matter of technical issues (which wouldn't matter if she was solo like Diddy) means you agree that series performance wasn't the factor here.
Its not a matter of me attributing her exclusion based on technical issues, but rather its a given fact at this point. Now while this is just a guess, what probably happened was that they were supposed to work like Zelda and Sheik, but followed each other around like the Ice Climbers thus being close to how they worked in DKC2, but you probably know that this is what I think by now. As it stands this, or whatever the real way Dixie was supposed to be added in, didn't work out, and thus she got excluded. Now in regards to this meaning that the performance had no issue here...yes, it didn't. Some type of error caused it to be messed it up, but I don't really think it hurts the theory, since it was an outside problem.
- Fire Emblem trio: You conceded this one, right? Gonna assume you did for now.
Maybe. It sort of depends on what cut out Roy. If the development team thought that the FE series simply had too much, or there was a crunch for space, I think it would fall in line with my theory. If he was cut for a technical reason, like Dixie's was, then it would go against it.
- Mac: You skipped it, but Punch-Out still had a comparable but better history than Metroid and outdid both retro series (even predates them). Obviously series performance wasn't stopping Mac back then.
I skipped this? I didn't mean to. Anyways, it is curious why Mac was never included. When Sakurai talked about other retro series, he never seemed to mention it. Heck, there are no Punch Out stickers either. Whatever the case though, PO's old sales don't really have much to do with a debate on curent performance, since they had all happened in the NES days. It was a retro series at the time, and prior to Punch Out for the Wii, was one that changed main characters. Retro characters inclusion doesn't seem to work with sales, nor does it seem to work with straight up popularity. I suppose I have to concede that its just random with them, but hopefully Little Mac can get in now since he's not completely retro anymore.
- Zelda vs. DK in Melee: You can make the argument that the two were at least comparable, but DK had the better track record. The only thing Zelda had over DK was that OoT was more recent than DKC1 (and DK64 was no slouch either). Impossible to justify with series performance.
LoZ also had MM come out recently too, as well as the Oracle games and LA Dx, so if you count the sales for the generation, it was doing better overall. Given how this initially got them the addition of Zelda/Sheik, and then latter the two clones, I think it falls in line well enough. This does lead me to another observation though in that DK64 was pretty under represented. While it allegedly got a stage in the form of Jungle Japes, there was no real location like that in the game, and just had the same name for some unknown reason. No real trophies for it either at the time of Melee, though I suppose you could say K.Rool could pottentially have been.
- Mother: Like Fire Emblem in that it's (mostly) JP only with niche sales, but with fewer games. Definitely not series performance.
On further reflection, you're right here. This shouldn't have been series performance, at least with Lucas. Back in the day, Earthbound was pushed as a big game, and Earthbound 64 was coming out (har) so Ness doesn't seem like that odd of a choice if he was all on his own. On his way to Melee though, Sakurai actually stated that he wanted to put in Mother 3's main character in Melee, isntead of Ness, but obviously couldn't. When Lucas finally did get his game, and Brawl came out, he got in and Ness wasn't cut. Thus Lucas probably got in just because Sakurai wanted him to get in, and it didn't matter that much with sales. Still, even though I acknowedge that it was probably just Sakurai, it didn't really screw all too much with the theory, because the previous series that only had one character, but had higher sales (F-Zero, Yoshi, and Metroid I guess) have character issues, which Mother doesn't really.
Anyway, assume Mario (not counting the Wario situation), Pokemon, Kirby, and Metroid fit your theory.
That leaves Zelda (over), DK (under), Wario (under), Star Fox (over), F-Zero (under), Fire Emblem (over), Mother (over).
4 vs. 7, sounds pretty solid to me. Probably helps that most of the roster explanations people believe (including yourself) revolve around the characters themselves rather than the series.
As I said, I don't really think LoZ and DK are wrong when you consider the timeframes. Wario's pottentially under (depends on how your view is on where the series split from Sakurai's perspective) SF is clearly over, F-Zero simply has character issues, and I don't think FE, Mother actually have problems, even if the reasons are dubious for character inclusion. Thus...well its as I said before, the only thing that really doesn't make sense to me here is Star Fox (And Mother, but that worked out)
Get out of my head! 
