Yeah, I think Metroid Prime surprised everyone. I mean, who thought an unknown developer in Texas could bring Metroid into the third dimension without sacrificing any of its essential qualities? I'd also never played anything so immersive. It felt like you really were Samus. I remember the first time I saw her eyes reflect in the visor after a big explosion. Just incredible. The graphics were also great and the music fit lonely Tallon IV perfectly. Man, such a great game!
The linearity of Fusion didn't bother me when I played it because, for whatever reason, I didn't yet associate open-ended exploration with Metroid, despite all my time playing Super Metroid. So I enjoyed it right away. I really should go back and play it again...
As for Other M, you just have to know what you're getting into. The moment-to-moment gameplay is different but a lot of fun. They more or less preserve the exploration the series is known for but they have a tendency to tell you where everything is via waypoints on the map. Prime did that too but only if you wandered around for a while without accomplishing anything. Other M makes it ubiquitous but I think there's an option to turn it off entirely. Don't expect anything good from the story and you should be good to go 
