Metroid's timeline is pretty straightforward compared to Zelda's:
Metroid: Zero Mission prequel manga
Metroid Zero Mission / Classic NES Metroid
Metroid Prime Trilogy
Metroid II: Return of Samus
Metroid III: Super Metroid
Metroid: Other M
Metroid IV: Metroid Fusion
Most of the games clearly indicate where they fall in the timeline of events, either through contextual references, or through direct flashbacks to the previous stories. It's much easier to keep track of than, say, Castlevania.
The Zelda chonology, on the other hand, is a total cluster***k. Just for starters, Nintendo of Japan and Nintendo of America don't agree on what order the Zelda stories are supposed to go in. Not a good start. If that's not bad enough, the official Japanese timeline
splits into two paralel universes! Then on top of that, you've got the Game Boy classic/color and Broadcast Satellaview games--while generally considered canon, even the people in charge of the Zelda story line admit they have no idea when most of these are supposed to take place!
SPOILERS:
BurningDoom wrote:And Link's Awaking is all a dream so it never really happened.
Except that the Wind Fish still seems to still be around at the end, so maybe it sort of did happen, somehow, sort of... don't you hate when they do that?