One must keep in mind the mentality of things, though! Who knows how long it would be until we see a newly published "low glitch" run, and if it would even pass the extreme burecratic process (no, really, that's basically what waiting until it gets submitted until deciding if we should have separate categories is). The difference between Chrono Trigger and Earthbound is that the Earthbound run still stands as being fairly impressive today, whereas CT was beaten by a mere ordinary speedrun (so the obsoletion made sense).
The intentions of a movie mean nothing! Absolutely nothing! How it plays out is what matters. If I made a TAS that set out to make people want to watch it while taking a shit, and they instead watched it while doing trigonometry, a faster movie that did make people want to watch it when taking a shit shouldn't necessarily obsolete the older one; because it's still good, and the new one isn't necessarily fun to watch while doing trigonometry. It's crude, but here's another example: you have a run that very obviously does something much differently from a new run, in a way that almost-if-not-completely changes what happens in the movie. I'm talking story-skipping or game-breaking type stuff. The old run is still impressive, but should the new one necessarily obsolete it? They're still around, yes, but they don't get the Torrent encode support that the non-obsoleted versions do, and they're usually kept "hidden", so to speak (I can remember one movie that did mention and link to an obsoleted run in the description, but that's it). It might not be the best impression to give off to new visitors, you know what I mean? "Oh, they played this RPG I like. But hey, what's this? ...okay, this is kinda cool! But why don't they have runs of RPGs that don't do all this crazy stuff?" It might give them the wrong idea, that we don't have full game runs of longer movies.
And as I mentioned, having strict definitions isn't always the best choice. There's a distinct time difference between the two implicitly proposed any%, best time through any means, and 100%, best time without this staircase glitch. We have had many runs that were "low glitch" in the past. Link to the Past probably being the best example - it's actually a perfect comparison. I believe the warp-to-below-the-screen glitches are disallowed in "normal" runs, but it doesn't mean they obsoleted the normal one.
Too extreme for you? Okay, how about Pulseman? The glitchy run didn't obsolete the not-quite-as-glitchy one in this case (mostly because none existed before then), but the not-quite-as-glitchy one came later and was accepted. It's precident (and not overly dated precident either)!
Or how about Dragon Warrior 3? This may be most damning of all towards the obsoletion argument. The glitchy run came after the not-quite-as-glitchy run, but didn't obsolete. Yeah, the two came within close proximity of each other rather than one being three years older, but it still shows my point.
So what is my point, you ask? Well, best case: keep both runs, and worst case: obsolete, but officially state outright that runs that don't use the staircase glitch are still allowed, no questions asked, and no discussions "deciding to have a no glitch any%, 100%, an "all aspects" type category, or none at all." Glitched and not-quite-as-glitched (not "no glitch any%", which I might mention sounds pretty lame) have been allowed in the recent past - especially with game-breaking glitches - why bother having lengthy arguments about whether they should be allowed now? Changed standards or not, it's still pretty ridiculous to either limit people to using all glitches game-breaking or not to get as fast a time as possible, or to use no glitches, go for 100%, or to do "all aspects" (what you're allowed to do to do all aspects being seemingly intentionally debatable).
As for what defines a category seperation...stop being so institutionalized. :) There is a definition out there, I'm sure, but explaining it and debating over it is pointless, as common sense can dictate it most of the time anyway.
So yeah, if we absolutely must obsolete the old one, make it perfectly clear that runs that don't use the stairway glitch are still allowed. Because they should be; there's no sense in arguing over that point IMO, much less saving the argument until a new run that doesn't use it comes along.