You can catch him in a
Dive Ball if you like, but he has a CR of 3, just as i said, making him one of the Hardest-to-Catch Pokemon Ever.
Also, he has Recover at Capture, so make sure he STAY at low health.
Now the 4rd gen move Heal Block would be useful, but the 2nd gen move Taunt would also work...
???
A Dive Ball is equal to a regular Poke-ball, unless it is used on seafloor Pokemon (Clamperl, Relicanth, etc.). That makes it extremely useless against a Mewtwo, let alone any other high leveled non-seafloor Pokemon.
Besides that, Dive Balls aren't even available in FR/LG. Dive is no longer used as an HM, and all of the underwater elements were taken out. The only place any are available is in Mossdeep City, in R/S/E.