And I, as the DM, can think of dozens of ways to neutralise that and not allow it to be an overpowered benefit that circumvents the rules.
How exactly do my examples circumvent any rules? Either the PC shapechanges into a rat, or he doesn't.
Then again, are any of those things so bad or broken that you would disallow them? Seems like a lot of fun could be had with all those examples.
Actually, I did disallow the Dead Rat Deserter Theme in my upcoming campaign, but that was partially for other campaign reasons as well.
But part of my issue with themes is one of balance. I see a lot of imbalance in many of the themes and have a bit of an issue with handing out the equivalent of free magic spells via themes. In Champions, x-ray vision and time travel and viewing into the future or past, and other types of powers are cautioned against because they can unravel the mystery of the DM's story. I see an At Will power where a PC can change into a rat and infiltrate basically undetected into many scenarios as potentially unraveling the mysteries that I put into my game.
Levitate is a 6th level Daily power that is only slightly more powerful than Levitation. Levitation, on the other hand, is an Encounter power, so it has more utility in some ways. And Levitate has a cost (i.e. using up a 6th level Daily power slot).
I'm just not keen on handing out free magic spells to just any PC without a real cost. For example, before the Bregan D'aerthe Spy Theme came out, a non-Wizard PC had to pay two feats, an Int of 13, and using up their only multiclassing feat to acquire Levitate. Now, they can get a slightly watered down version of it for free.
To me, it's just the re-occurring bigger, badder, better aspect that WotC continues to flood the market with.
Personally, I think that Themes are a good roleplaying story hook idea, but a terrible "let's just keep giving PCs more and more abilities, and making them more and more complex" idea.