Minor glitches should be in Category:Minor glitches along with Category:Minor glitches (version).
Although there seems to be no consensus on what exactly defines minor. I'm probably going to suggest it be defined as a graphical glitch that has no effect on gameplay, with "headline"/"major" glitches being the standard Old Man, Ditto, Mew, Q glitches, and categorized as Category:Major glitches and Category:Major glitches (version). Glitchdex pages will be in their own categories.
"Miscellaneous glitches" seems to consist of glitches that do affect gameplay in some small way, but if the distinction is not clear enough we can merge this with minor glitches.
"Speed runner glitches" are glitches that simply help the player get through the game faster, like Get Past Marowak without Silph Scope or Get Through Cycling Road without a Bike. We could also merge this with minor glitches.
A lot of articles are about effects of the glitch attack known commonly as "Super Glitch". What I think I'll do is just merge all of these effect articles into the Super Glitch article.
Finally, 'dex entries do indeed get "Category:Glitch (Pokemon/attack/item)" as well as "Category:Glitch (pokemon/attack/item) (version)" and will most likely use the Glitchdex 2.0 style designations ("RB:000") as pagenames.
I count fourteen uncategorized articles in Special:UncategorizedPages
Bird Type - "Beta information (Red/Blue)", "Beta information (Gold/Silver/Crystal)"
Codebreaker - "Dictionary"
Ditto Trick - "Major glitches (Red/Blue)", "Major glitches (Yellow)"
Main Page - probably does not need categorization
PokéPC effect - not sure, this is an effect of Super Glitch so we'd have to decide where Super Glitch itself falls within the spectrum
Pokémon Cloning - index of cloning tricks, maybe it gets "Major glitches" or we give cloning articles their own cat
Pokémon Cloning (Emerald) - "Major glitches (Emerald)"
Pokémon Cloning (Generation I) - "Major glitches (Red/Blue)", "Major glitches (Yellow)"
Pokémon Cloning (Generation II) - "Major glitches (Gold/Silver/Crystal)"
R/B Name Generator - probably does not need it, but "Tools" if otherwise
S.S. Anne Ship Truck - "Category:Beta information (Red/Blue/Yellow)" assuming this has something to do with the R/B/Y beta, I forget
Screwed-up sounds effect - superglitch effect I believe, see above
TMTRAINER effect - "
Tasks - does not need to be categorized, but if need be I'll move it into the project namespace
As an aside, we're using Extension:FlaggedRevs to ensure all content is accurate. Registered users can make edits to a draft version of an article, but only sysops and "QC" users can approve them to show up as "reviewed edits". This was done because one of the concerns we had was that someone would put false information and no one would bother to check it. The problem we have that other wikis typically do not is that our information is pretty much original research. Even Bulbapedia and Sonic Retro, which are more specialized than Wikipedia, don't tend to have that problem because much of the information is somewhere else. Wikipedia explicitly denies being responsible for any entries and expects contributors to cite sources, but we don't have sources to cite because we find all of this out ourselves. Thus, we have our staff oversee and verify everything that gets put on the site so that we can say we are responsible for our content.
We had this sort of thing with "Submit a Glitch" in some way, but there was an enormous backlog at times because staff would approve of a glitch but not add it to the site. With this system we can allow users to directly participate in the site whilst not compromising our integrity. While we are volunteer staff, we hold ourselves responsible for the content unlike Wikipedia's sysops.