JOJA. Villagers don't change scedule, you can still complete bundles and chase after rewards, save for a last one before getting the Joja membership, you can buy autopetters at will (they are a very rare drop in Skull Caverns, otherwise), the Movie Theater lies in a more convenient place, J-Market is still around and is open many hours in a row till 23:00 (plus it sells sunflowers cheaper) and your "Perfection Trophy" not only is decorative, but produces Joja cola daily, on top.
There are no serious changes or nasty side-effects, for choosing any side! Junimos still work for you, from huts and all NPCs are the same!
Pro tip: Make sure to complete the Bulletin Board bundles too, before going Joja. Grandpa's evaluation skyrockets! Just leave one last, tiny bundle undone, before buying the membership, from Fish Tank bundles ideally; choose one the reward of which you don't need/like.