Has there ever been a better ending to a Master story than the one seen in The Sea Devils? Forget about why The Master would have a mask of his face on his person (although carrying these things around seems to be a hobby for him. Look at Terror of the Autons). The sudden realization from The Doctor that the man on the stretcher is not The Master, then look up to see the real Master waving and driving away in the hovercraft more than makes up for any supposed plot holes. It's also rarely satisfying to see The Master "win", but also be able to rub it in a bit at the same time.
For a Malcolm Hulke script, there isn't as much of the morality play at work as in other Hulke stories such as Doctor Who and the Silurians and Colony in Space. There is a brief moment in Episode Five where it looks like The Doctor has struck a peaceful alliance with the Sea Devil leader, but those hopes are soon dashed. It's no surprise, really. Despite The Doctor's best intentions, the Sea Devils are thinking of war right from the outset. They are often the first to open fire when they meet humans (as well as a Sea Devil's first meeting with The Doctor, where the Sea Devil fires at an unarmed Doctor). The Doctor is fighting an uphill battle in trying to achieve a peace between the humans and the Sea Devils.
The Sea Devils is a truly fantastic story - easily the gem of Season 9, and certainly the best story thus far in the post-Season 7 Jon Pertwee era.