What if, instead of changing the HMs we have, we keep, say, surf and fly, but then make all NEW HMs, which would be more powerful and have different uses. A fire-type one to melt down metal stuff. An electric type one to open electronically locked doors. A psychic varient which would do something similar to strength but with the mind. More type variety, and maybe actually make them decent in some aspect, such as:
Melt away: A decent fire type attack which remove's the opponent's held item.
Code break: Lower's the opponent's highest stat by 2.
Mind Force: A powerful move which has the possibility of flinch. Like protect, it is less likely to work twice in a row. The turn after this is used, the opponent is immune to physical attacks. (As it has been thrown across the stage, moving it out of range from physical attacks.)
Thats another idea they could use: Range. Mind Force wouldn't need this to work, but here's how this would work: Along with attacking, pokemon could move closer or further. Some moves/types could work better depending on the range and how far away you are, and some may not work at closer range, while other moves/abilities could move something close or push it away. Probably won't happen, but it's another direction they could go.
EDIT: This definitely won't happen if how the battle system is designed is any indication. But still, a cool idea nonetheless.