I despise the low use of Waterfall in-game outside the battle: often, you have to use it only before the League and not much else.
Luckily, it is one of the few HMs useful even when battling.
I'd like to see much more areas in-game before the League not explorable before and -if possible- relevant for the plot.
I'd even wish to see the HMs Whirlpool, Dive, Cut, Rock Climb revamped; some ideas:
(1) Whirlpool makes sense as the Water type version of Cut (which gets rid of basic obstacles) but it should have more room in the plot. Low usage in-game = annoying when you have to use it.
(2) Dive, such as Rock Climb, has the potential to expand explorable areas from the earth/soil and the surface of seas/lakes to the deep sea but, in actual fact, it is a filler move.
(3) Rock Climb has the same problem: good idea to make mountains more useful, but low practical use (albeit greater than the Sub's one in HG/SS).
I want to see some changes into the HMs:
* Strenght, which should include the effects of Cut and Rock Smash
* Surf, which should include the effects of Sub and Whirlpool
* Waterfall is ok, but more usage really makes the difference
* Same thing for Rock Climb
* Fly is always good
I want pokemon games be similar to the Legend of Zelda ones: you have basic items/abilities, but a ton of upgrades. That's only my opinion.
The Grass-Fire-Water trio makes sense for a beginner, but a fourth choice seems interesting. A sort of what happens in Pokemon Yellow, but without being forced to pick Pikachu and with the possibility to pick a good 3-stages pokemon of the region (maybe a Normal type to avoid being broken) such as Lillipup. This allows the player to begin the plot in an unfavourable position due to the lack of super-effective STAB moves.