The original OFU spelled Missingno without the period at the end. It's not strictly how the name appears in-game, but it's just as valid a spelling as MissingNO or MissingNo. or any of those other spellings that people use because the Kanto games predated Pokémon's use of consistent punctuation and lowercase letters.
I'm not seeing much other than choppy sentence structure and being very attached to their author for unique mini-Missingno activity. Were the other OFU minis just incredibly bland? I suppose it doesn't help that the Pokémon OFU only has two published chapters before vanishing completely, so we don't get to see what might have been.
Besides, I was thinking more along the lines of what they would be capable of. Teleportation, duplicating items and movesets, Water Gun, and Sky Attack are pretty much the only things set by the games they appear in, which is both disparate and lacking by Pokémon standards, and their reputation as a glitch might mean someone might give them any number of new abilities and attribute them to "glitch powers", when a canonical entity should be diminished in power to make a mini, not increased. They aren't very well established, essentially. Rayquaza and Deoxys might have been left by the wayside in favor of new properties, but Missingno was never canon at all, and could only even be considered so within a very small time frame, since even the remakes of the Kanto games retconned Missingno and its cousins out of existence. That poses a bit of a problem.
Yes, that's the problem with Pokémon, isn't it? New games and movies and shows come out every year, and every three years or so they drag another few dozen Pokémon out into the light, leaving plenty of the existing ones unconsidered and forgotten about. The thing is, though, even if we picked something inconsequential like a mini-Luxio or a mini-Carbink, it would still be an improvement over Missingno, IMO, because it had an actual in-canon presence. Not that those two would be good choices, because they're not, but that's not the point. They do something, they have a well-defined power set, they might affect the average player's experience of the game rather than the experience of someone who went out of their way to create the conditions in which one could be encountered, and Missingno is so ill-defined that I'm not even sure how we'd decide which of its five primary forms an individual mini would take.
Mewtwo is another nice choice, by the way, since it's a presence in multiple generations of games as well as Super Smash Brothers Melee, has two movies and a television special dedicated to it, has well-established powers that could easily be toned down for the mini, and is a perpetual fan favorite. I'd cast my vote for that if we were still in the process of selection.
But regarding your last point, about nobody in the community actually being invested in this... (sigh) you're probably right. I'm probably one of only a few people who would give more thought than "Huh. Didn't that used to be something else?" if the mini was changed. I feel strongly about it to make another huge wall of text, but I'm well noted to offer hundreds of words of support to a number of doomed topics. I admitted then and now that Rayquaza isn't the best choice. Out of the three minis we have, I'd have supported Deoxys if it hadn't been apparently shoved off the table. But it's the choice that's there, due to multiple mentions in-story(not just Sylibane, either, even though I could only find one other example when pressed) and on the Board. Consistency is important, and consistency is the reason why we don't let anyone making a story in a continuum rewrite the mini as whatever they want when they want, even if the choice the second person makes is an improvement over the original. Rayquaza's not the worst choice, and though it is less diverse considering what we already have, it works well enough that I don't see any need to change it. Besides, the continuum will have multiple minis even if we decide to excise mini-Rayquaza from continuity, it's just that one will only exist in an OFU while the other exists both in an OFU and the Word Worlds for some reason.