I think there could be separate categories for both trilogies for people who want to run the game but aren't too keen on going for 3-5 hours for a single run, if they're doing solo any%. It would be slightly different than running the original game and sequel, I just hope it would be different enough to make it a viable option to add to the leaderboard. Could this be considered?

There's definitely enough differences for IT (Individual Trilogies) to be significantly different times. If enough people are interested in it or do runs of it I don't see why it shouldn't be added.

I don't believe that the trilogies are as deep a departure from any% enough to be their own category, especially not a main category. However, for those not as interested in doing the whole game in one sitting (It can be daunting if you haven't built the stamina for it), the game does have the super stories that are an easily learned and ran category on their own.