It just takes a lot more work to implement such a feature when it comes to 3D models.
Back in the days of sprites, all Pokémon fit within an 80x80 pixel window, so the items of clothing were one-size-fits-all.
I imagine was just an extra bit of data tied to Pokémon sprites to signify "this is where the Pokemon's head is", "this is their mid-section", "this is their paw/hand", and the items of clothing would snap to those areas appropriately.
Edit: There is a significant chance I'm mixing this up with Black and White's Musical dress-up, but I'm quite sure it's the same mechanics for DPPt anyway.
But for 3D models this becomes an issue. Proportions are now a thing, and the Pokémon are now in constant (if subtle) motion. So not only would every/most clothing item(s) have to work with every Pokémon, but they'd likely be clipping through the models as the Pokémon moved, depending on animations, etc.
It's a lot more work for a side-feature, though I agree it's a shame that it's missing! Instead they doubled-down on Ball Capsules for extra customisation, and at least they did a pretty decent job of that.