I think HMs are justified - you're supposed to be working together with your Pokemon, after all, which makes more sense if they help you with more than just battles - and my idea above makes them more convenient.
Creator of Jay's Journey (see quote!) "It's not ten years old! Therefore, it sucks!" - Nostalgia whores everywhere
Multiple difficulties available from the start. Magikarp(easy) Starter(normal) Fully evolved(hard) and legendary(super hard). Affects bosses and trainers teams/movesets, enemy levels and AI. Magikarp has moronic AI even moreso then usual. Legendary is like fighting a genius competitive level battler.