I had this problem, too. I eventually got it by doing the following. Once you have him down low enough on health and you have the stand, wait for him to do this one particular attack:
It's the one where he slowly flies towards you to shoot a fireball at you. You can tell when he's going to do it because it's the (only?) attack where you can see fire trailing from his mouth beforehand. You have 2 options.
I stood at the middle of the ship, and did a rolldodge left as he did the attack. I immediately threw the stand upwards and he was mine.
I think this one would be easier. When you are ready to grab him, stand at the nose of the ship. That way, when he starts flying towards you w/ the fire in his mouth, you can simply do a double jump and throw it at him before he launches it.
As redshift stated, the fast-fall is NOT your friend. If you screw up the fast-fall after capping Meta Ridley, you have to do the whole level again. This is especially irritating on Intense.
Redshift: You said you don't lose stickers unless you "see" the game over screen? Is there a way to bypass it, or something? *remembers all the times he saw 10+ stickers fly away*