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.
Yeah, it's a shame they removed such sequence breaks in Metroid Prime Trilogy, and it's the main reason I can't think nearly as highly of Prime as I do Super. Whereas Super feels like it actively wants you to break it, the Prime games have quite openly made attempts to limit player freedom, and are ultimately very linear experiences. For Prime 1 and 2, at least, it doesn't feel linear the first time you play them because of how expansive the world is, but you're forced to pick power-ups in a specific order - for Prime 3, of course, it is linear and it feels linear too. It's a game I liked a lot when I first played it, but going back to replay it was a big mistake.