Thanks man.
When you finished the game once on a real PSONE, you saw the ending, right?
From a similar topic, i read that someone already used a real game copy on an emulator but still didn't see the ending.
Anyway, I found in Youtube this video:
It looks like this guy is using an Emulator and I'm very sure that he was able to finish the game once and was able to save it coz he's using a VF-22 on an early stage / mission.
Regarding the underwater satge, I was also having a hard time till i saw this video:
Check it out. you might want to pick up your PSP and play to finish it.
And let me know if you see the ending.