Metroid Prime 1 didn't seem to be quite as bad, but there were still issues. There's a boss that's pretty far from a save room - first you have to fight your way to him, then after you beat him, you have to fight your way back. Get killed, and you have to beat the boss again. Most bosses are right next to a save room but not all.
I didn't play 2, but 3 was definitely worse than 1 with regards to save rooms. I despise the idea though. I really would have liked for them to put about twice as many save points in the game, or better yet - give you the ability to save whenever you want. Save rooms also restore full health and missiles, but they could have added the ability to save without restoring your health.
FWIW I enjoyed MP1 a whole lot more than MP3. I mean, I actually beat the game rather than quitting in frustration. However, my bullshit tolerance has gone down since I played MP1 so I don't know.