Sure, you don't turn into valor anymore, but it didn't make sense why Quinn disappeared anyways
Eh, lots of things in League don't make sense though. Tahm Kench ulting on dry land, Jinx somehow fitting a mega rocket into her tiny gun (same with Ashe and her giant arrow), Skaarl "disappearing" when his health depletes, to name a few. In all of those cases, we're supposed to take logical leaps and assume certain things are happening even if the animations don't support them (i.e. we have to pretend Tahm Kench is traversing the river even if he just dove headfirst into the concrete, we have to pretend Skaarl is actually hiding in a nearby bush even if his model isn't physically there, etc).
I'm sure if Quinn's old ult actually had an animation that showed her leaping out of sight before Valor swooped in to take over it would have made much more sense visually. For example, they could have made it so that upon pressing R, Quinn's model latches onto nearby terrain (maybe like Camille in the middle of her hookshot) while Valor comes down from the sky to take her place, and then upon reactivating R Quinn leaps from that piece of terrain and dives down in a hail of arrows upon Valor's location.
Idk, I just think a lot of the confusion regarding Tag Team was due to it not being supported by the proper visuals. It looked more like she was transforming into Valor than swapping with him which is obviously a problem in terms of understanding what the character is doing.
Also I just want to point out that just because Valor is in all of Quinn's abilities doesn't really mean it makes him feel like an actual character. Right now Valor is a particle effect, nothing more, nothing less -- he's an animated image made to decorate Quinn's abilities, rather than an interactive in-game entity with his own abilities, stats, etc that the enemy is forced to deal with in addition to Quinn (which is ideally what he should be rather than a bird-shaped missile).
Not to mention that if something is important and characteristic enough of a Champion, those things are worth keeping -- once again, like Gangplank's oranges. You wouldn't expect a murderous, badass pirate to be peeling citruses in his spare time and eating them to cure disease, or laughing while raining a barrage of cannonballs across the map from seemingly nowhere. But that's what he does, that's what players love about GP and know him for so Riot decided those things should stay. I'm not sure why the same courtesy can't be extended to Quinn and Valor.