Thank you for the suggestions, though some of these would require extending the save data block which would apparently remove backwards-compatibility of save files. For example, to add more trainers without changing existing trainer data instead would mean that more 'flag' triggers (whose statuses are stored in the save file) need to be accounted for. This is also the reason why I've decided against extending the PokéDex until I have the time to use the idea in a separate fork of the project.
However, the "random trainers" thing sounds doable, I'll mess around and see if I can create a battle with randomized lineups. Though, I'd have to do this later as I have my hands full for now. I also already have a plan to use the Trainer House in Sootopolis City for custom trainers who you can battle once per day.
For now, there are actually some good training locations with higher level Pokémon to battle in the currently posted update. The Sky Pillar has had its levels boosted to be like it was in R/S; Altering Cave, Navel Rock, Faraway Island and The Moon have their own special encounter lists.