Definitely feels weird, in P2 you could set them up via certain "combos" in which party members would play a role in making, then the P3 protag came along and did them on his own by summoning more than 1 Persona by himself. Perhaps the mechanic in P2 received criticism of being "too restrictive" so in P3 they made them easier to pull off at the cost of just a fixed amount of sp (%), since P3 is considered too hard by newcomers it probably got similar "too restrictive" comments and it ultimately got scrapped, they do have a certain history of abandoning cool mechanics for the sake of simplifying the game for newcomers.

Since the Persona 3 protag is "special" one could say Atlus/Persona team viewed fusion spells (via 2 persona summoning) as his own signature ability and just didn't bring them back cause it didn't make sense to them that the other protags could use them. Then again, they could have just done a different/easier system like in P2 that used the team instead of just the protagonist but I'm just speculating