Why do you think gen-specific Pokemon pairs get unequal treatment by Game Freak? (Eg, Vileplume got a new evolution in Gen 2, while Victreebel got nothing, and Whimsicott was already better than Lilligant even before becoming Fairy-type in Gen 6.)
I suppose because those pairings don’t serve any gameplay purpose beyond the games in which they were originally introduced. Oddish and Bellsprout were no longer version-exclusive in generation II, so why continue to act as if they were? If anything, I think it would be pointlessly restrictive for future games to demand that those pairs of Pokémon continue to mirror each other. If you have an idea for an alternate evolution for Gloom that you think is a good one, why declare it invalid because you don’t have an idea for Weepinbell? As for Whimsicott getting a buff that Lilligant missed out on by becoming a Fairy-type – well, you’ve hit the nail on the head. Whimsicott was already better than Lilligant, so clearly they didn’t care in the first place. Why would they care more in generation VI, when Whimsicott’s special relationship with Lilligant was no longer relevant, than they had in V?