The problem with SR-ing Deoxys is not that he's hard to catch (like mentioned above, you might as well use the Master Ball, because the rest of the legendaries are a much smaller pain in the butt), but the fact that you also have to catch Rayquaza, fight Zinnia and watch a 10-minut-long cutscene before you can actually see his stats. Oh, and the game defaults to Rayquaza as your lead, even if it fainted during the Zinnia fight, so no Nature manipulation with Synchronize.
I just reseted the game, SR-ed Rayquaza properly (who CAN be Synchronized and his stats CAN be viewed during the Zinnia fight) and then caught Deoxys without worrying about Natures and IVs. He turned out Lonely with crap IVs at all the important stats, I don't even care.
See, we can get so obsessed with the technical aspect of the games sometimes, that we forget to feel like little kids again and just enjoy the awesome. Awesome as in:
[fanboy_mode_on]
Oh WOW! I'm in space! I'm in space wearing a spacesuit, riding space Rayquaza! I exploded a space meteorastrothingiroid and space Deoxys came out of it! And this is in-game not some stupid event that I can't get because it hasn't come out in my country! And I'm fighting him in space! Spaaaaaceee!!!
[fanboy_mode_off]