The oddest thing I can think of is probably that in FRLG it was impossible for Gen I Pokémon to evolve into their gen II evolutions before obtaining the National Dex. I'm fine with not having the possibility of breeding them because the daycare is only reached later, but not being able to evolve them was incredibly weird. Just like not putting the time feature in those games and preventing you from evolving Eevee into Espeon or Umbreon.
I would say the same thing for not having cross-generational evolutions in LGPE; while disappointed, I could understand not having non-gen I evolutionary lines, but not having cross-generational relatives makes no sense, especially when Alola forms and Mega Evolutions are in.
Also, having certain features in some games and not having them in others is weird or at worst annoying. The VS Seeker is really a thing that should have in every game since it was introduced, just like gym leader rematches. I especially find this annoying considered they randomly scrap these QoL improvements and yet they bother introducing evolution-inducing held items just for trading or incenses, or whatever gimmick evolution just to somehow "justify" evolving a Pokémon through trade or breeding a baby Pokémon when it was not possible in the prior generation(s). Also, gimmick evolutions on their own imho qualify for these weird design choices. Many of them at least make sense, but others like game-dependant ones, Inkay which evolves by having the 3DS held upside-down, Feebas's beauty-dependant one, and those that evolve while trading with certain items imho don't. One of my hopes is that in a future generation they'll cut the number of those, giving them normal level up evolutions (or at least friendship- or time of day/weather-dependant ones).
DPP's poor integration of the touch screen could also count, but especially DP are clearly built following what they already had with the GBA games so that it's understandable that they focussed on making it work on the DS's "normal" screen first, and thinking about how to best use the touch screen later.