The discrepancy is the fact that it's near impossible to get a perfect read on their IV's if you're going for something like Hidden Power, or they're at a level where 30-31 is hard to narrow down via EV boosts, not to mention huge gaps between being able to check them in case of a reset for a bad nature or wrong IV's.
- Reshiram and Zekrom send you right into a battle with N that auto-saves before you get full control of your character again
- Xerneas and Yveltal force the battle with Lysandre
- Rayquaza has the Zinnia battle
And while there are other options, some other legendaries just have annoying gaps if you don't want to get them in post game
- Groudon and Kyogre have the 5 minute cutscene
- Even if you wait for Sky Pillar to reset Deoxys, you still have Rayquaza to go through.
While it makes things more cinematic, they really should give us a few seconds of gameplay to let us save before battling the Legendary and right after so we can check its stats and reset/save. Or just have the Legendary come with perfect IVs (its not going to matter, we can't use them in the Battle Maison anyway and even if they get horrible IVs they can curbstomp the Elite Four and Champion). Give us a chance to try and get them with good IVs or have them come battle-ready, otherwise you're just making things more difficult than they need to be.