Alternate ending #3: you edit the maps on the ROM so that there's no necessity for HMs, as it was in the Crystal Clear hack.
This would involve things such as removing HM-related objects (cut trees, strength and rock smash boulders), making bridges over water, and possibly coming up with more unique options to get to water-heavy areas. Alternatively/additionally, have very easy access to a Move Deleter and/or Move Reminder.
Crystal Clear, as you know, did all of this very effectively: it removed most boulders and cut trees, added in small land bridges in some places as well as paths to get around waterfalls, and rigged up an easy ferry system that would take the player to areas such as Cianwood City and Cinnabar Island. You only needed HMs for fully optional content such as the Dragon's Den*, the Whirl Islands, Mt. Mortar, and things like items behind cut trees or rock smash-encounter Pokemon.
You never had to use HMs if you didn't want to, and the Move Deleter was accessible from early on rather than at the end of the game. In my recent 100% playthrough, the only HM I actively used was Surf, but I could easily swap other HMs onto my team thanks to there being a Move Reminder NPC in the game to re-teach whatever move I deleted.
* yes I know it's not optional in gsc + hgss, but in Crystal Clear, it was edited so Clair just gives the player the badge rather than sending them on a proof of worth quest. bless