Aiedail256: As other commenters have pointed out, there are more additions to Samus' movement capabilities granted by the morph ball than just fitting in small places. And to make it relevant again, all you gotta do is retcon it to be smaller - say 14" in diameter? And as for how she'd fit into THAT, I'd put forth the same theory as I do in response to being asked where she keeps her beams, visors, hundreds of missiles, etc.: go all-out and say that the Chozo were advanced enough to make a powersuit that can reconfigure the subatomic structure of stuff - or maybe even leverage E=mc^2 - on the fly without breaking a sweat, i.e. stuff gets converted into denser stuff or even "pure energy" in order to save space. Pop Metroid Prime back in, go to Samus' list of gear on the pause screen, select the morph ball, and zoom in on it. There's nothing but light inside!

The more interesting question is, how does Samus even MOVE while in morph ball form without breaking conservation of momentum? My guess is, the same way as the Hubble telescope rotates - changing the RPM's of heavy spinning wheels on the inside.