I could not agree more. Here's the general plot (spoilers ahead...yeah right) to the Metroid canon without the Prime series:
1) Samus is ordered by the Galactic Federation to go to Zebes and destroy the Metroid threat, and Mother Brain, leader of the Space Pirates, who don't even show up in the original game.
2) Samus is ordered by the Galactic Federation to go to SR388 and destroy all the Metroids on the planet, hopefully causing the extinction of the species. Samus kills the queen only to find a hatchling, who sees Samus as its mother (groan). She takes it back to the Federation.
3) The Pirates finally reveal themselves, steal the baby, and Samus...goes...and...gets it back? The Hatchling destroys Mother Brain but sacrifices itself in the process. So sad.
4) Samus is infected with the X Parasite (worst...name...EVER), which is thriving on SR388 now that the Metroids are gone. Samus is injected with a Metroid serum, made from that hatchling's DNA, and becomes half human, half Metroid. Or something. Diffusion Missiles are the ultimate result (sigh). Samus discovers that the Federation is cloning and breeding Metroids for military purposes. Samus blows up the station and with it, SR388.
WOW. I mean, that's a NOVEL right there. DANG. So many PLOT TWISTS. So much...so much character development. Tolstoy WISHES he could write that kind of nail-biter.
Get real. Without Metroid Prime, the series would be DEVOID of any sort of mythos. Thanks to the Prime series, we know detailed information about the Pirates and their motivations. We know a LOT more about the Chozo and Samus' origins. We know about Samus' involvment with the Galactic Federation and with other hunters. We know a lot more about Metroids and, thanks to Corruption, Mother Brain.
I can only hope that Nintendo capitalizes on all this backstory in their next (presumably) 2D Metroid game. The Metroid series doesn't have to be Metal Gear Solid, but it doesn't have to be Pac-Man, either.