Yeah, the fact that HMs are needed to get through the game, and are consistently not easily to delete, I think is purposely done to provide a challenge of sorts. An unnecessary one, perhaps, but one I've kind of grown to just get used to and don't mind. It's kind of the fun of it, imo.
Does anyone miss the mail thing you can put on your pokémon with a message on it? It's a little useless sure, but it was fun! I'd like to see mail back again.
I actually think mail would be interesting combined with wonder trade. Send random notes to random people, or some tactical notes on how to use some of my weirder breeding creations. (Current project: Counter/Focus Sash Charizard - Try spamming Rock Slide now, Choice Scarf Landorus!)
Here is what I want
Ash-Greninja Mechanic
Grass/Fairy Celebi
Mega Roserade
Wild eggs
Pygmy sub species
And bump
Because I didn't feel awful enough already about forcing my pets to fight others and capturing them from the wild against their will, why not also steal the eggs you find in the wild?
While I actually like this idea a lot in theory, I think it's something that might encourage similar behaviour in real life because there are younger people playing who might not understand that it's not ok to go bother a real birds nest or something like that.
That's sort if implemented already with Pumpkaboo and Gourgeist, but I'd like to see other pokémon with different sizes too!