I played metroid prime before I had the opportunity to play any of the 2d metroid games. The only one I have even started is metroid fusion, and I got stuck on one of the bosses near the end and haven't gone back to it.
I would have to say that I haven't found exploring in fusion very intuitive either. I recall many times getting an ability that would have allowed me to explore a previous area better, only to be blocked off by a convenient explosion or elevator stoppage that forced me to go through a completely new area with no idea how I was supposed to get back later, resulting in what I felt was a very linear path that only opened up towards the end once you have everything! By which time I had forgotten previous areas and so would need to go through each area room by room to make sure I hadn't missed anything. Maybe the earlier ones do a better job. Having played prime on both the Gamecube (At least twice) and the Wii, I did find that by the end I could map out paths to get me from A to B in the quickest possible way. It wasn't quite so easy in Echoes due to occasionally having to switch between worlds, and Corruption took away the interconnection by having completely separate areas and being able to quick fly (with slow cutscenes) to convenient landing pads throughout the worlds.
It is a pity that the great visuals just go out the window with certain visors. They have the same thing in Echoes and corruption to some degree, although I think the echolocation visor is the worst for visual fidelity. I actually quite liked the xray visor aesthetic as the were very thorough, being able to see Samus' skeleton, stuff like that. For any teenager who wishes they could have xray vision, just show them the xray visor and say "Are you sure you want to look at skeletons all day?"