It's late for this now but spoilers ahead (probs worth changing the titleof the thread).
ZeZipster (or possibly Kindo) what would you have wanted? That Yuna not change in two years? That despite not being a summoner, or following the teachings of Yevon anymore she still wears the robes and uses the same weapons? That she decided to go undercover dressed as... herself? Seriously how do you picture it should have been?
Rikku hasn't suddenly become eye-candy either, I'll point back to the original intro FMV of her and leave it at that.
The clothes change system seems a logical progression if you introduce jobs. Weapons changed appearance in the original, as should characters who change their style.