What I usually do is I go into the fight with two of my 3 party members already dead, then once he puts up his tentacles behind them, I bring them back to life (Life 2 or Phoenix summon) and then he won't blow them out of the fight, as long as his tentacles are up from the ground behind them. Makes it easier to have 3 people, instead of just the one, otherwise.

FYI, I didn't find Emerald or Ruby "hard". I thought it took a while to kill them, but it wasn't difficult. Just very tedious.