I enjoy the Super Mario Bros movie in the same way that I enjoy the Flintstones movie -- it's a stupid, badly written movie that doesn't fit the mood of its source material, but it's got really nice set design. Flintstones had way better casting, though. And acting. And scientific accuracy.
To be fair, the source material for the SMB movie (ie SMB1) is pretty flimsy given that it's not a story-driven game (in fact, none of the main series Mario games are), and it would be very hard to make it into a decent movie.
Back to the question at hand, the obvious answer is no. Donkey Kong and Bowser are simply guest characters in the Skylanders universe, like Link is in Soul Calibur 2.