I understand how it can be weird, but there's really nothing about Prime 1 or 2 that'd make them non-Metroidvania. Prime 3, though, I'm not sure it quite fits into the genre.
Perfect. My easy definition for a Metroidvania is that you can go anywhere you want (pretty much) at the beginning of the game if you have the right ability. And seeing what people are able to do in Prime right at the first steps on Tallon IV (High Jump Boots Aquired!), Prime 1 definitely fits the bill. The separation in 3 on different planets and an external ship probably does break that formula, although to be honest I never bothered playing it after I completed it the first time on the Wii. It was a good game and looked pretty, but I missed the overlapping paths that the previous 2 had.