Yes, the Axis probably should have hada few more planes, but I don't think it was terribly outbalanced.
The Axis had an awesome plan of attack. As funked mentioned, the 308th was the unit that made first contact, and we made contact with what seemed like the whole Axis air force. From my perspective, we had about 3 minutes to find the Ju88s. We went left instead of right and got lucky.
Even with all defenders at Malta vectored to intercept the Ju88s, the Axis managed to hit their targets.