Two unneeded things in pokemon games in my opinion:
(1) Pokemon Contests
I feel like they belong more to the anime than to the game itself because you can simply forget them without consequences, but you can't do Contests ignoring the Gyms. I simply skip them all: they don't add nothing to the plot and they feel like they waste room for other things. At least, the Pokeathlon in HG/SS gives you the possibility to gain evolution stones "more easily".
(2) Some unnecessary HMs or HMs that are so weak you have to get rid of them if you need a 4th moveslot available
For example, why do you have to run Whirlpool + Waterfall + Surf when the only move you'll use is Surf? Waterfall is rarely used more than once (except you are going to visit extra areas, but...) in order to reach the Victory Road. Whirlpool is even more niche and has no uses outside of that. Luckily enough, Surf is still very good despite the competition with Scald...