1. You don't need an empty space in your party as like with Latios/Latias another party member will be sent back to the PC. I like to leave a space though as it saves a bit of time. Set your text speed to fast to skip through the cut scenes faster later on.
2. Have a Pokémon with Synchronize and the nature you want for Rayquaza in the first spot of your party. If you don't have a dedicated catcher such as Spore/False Swipe Breloom, make sure this Pokémon has 175 or more Speed and knows Thunder Wave. I used Alakazam, and then Hold Back Metagross (from the Mystery Gift event) to get its HP down.
3. Use Dragon Ascent with Mega Rayquaza to KO Deoxys. You will be able to rebattle it later at the Sky Pillar after you rebattle the Elite Four. This should allow you to use a different Synchronize Pokémon for catching Deoxys.
4. When checking Rayquaza's IVs, make sure you enter 4 Attack EVs and 4 Special Defense EVs into your IV calculator, to account for the EVs gained when battling Zinnia and Deoxys. Use a Reset Bag before EV training it.
Very useful tips! I'm sure this could help a lot of people, so good on you for compiling this list. :)
Also don't forget to use your capture power O-power for an easier time catching them.
Nice advice. :)
When I caught Ray, I IV'd checked him with the next battle before Deoxys, I assumed it was the nature I wanted with my sync, and if the caculator came back with an error the nature would be wrong.
Its worth mentoining Kyorge and Groudon also respawn, and it's probably better to do them after the Elite Four considering the length of the cutscene before and after.
Also having the move Protect will allow you to avoid damage from Fly completely, this is necessary when using Breloom as it can't take a Fly at all.