No. You need to use the Eon Flute, which is given after defeating/capturing Kyogre/Groudon, to fly on Latios/Latias to Mirage Islands. If you have Omega Ruby you can only use Latios, and in Alpha Sapphire you can only use Latias. Also a fun tip, while flying on Latios/Latias pressing some buttons can make the Pokemon do different tricks.
Also even though you don't have your Latios anymore, Stephen will still give you the Eon Flute, meaning you can still soar on Latios without the actual Pokemon in your save file.