Hmm.. well the only Metroid games I've played are the (relatively) new ones:
Metroid Zero Mission
Metroid Prime 2
Metroid Prime Hunters
Metroid Prime 3 <-- I haven't finished this one yet
And out of all of those, I have to say that the only way to get a perfect representation of the series is to play it from beginning to end, as this series evolves from each game to the next.
If you're looking for just one great Metroid game, however, here are quick summaries of each:
Metroid, Metroid 2, and Super Metroid are the classic, (sorta) genre defining Metroid games;
Metroid Zero Mission is a retelling of the original NES Metroid;
Metroid Fusion is the transition between old Metroid and new Metroid;
Metroid Prime is where the Metroid series takes a big leap foward and evolves into a 3D First-person Adventure, while still staying true to the feel of all the previous Metroid games;
Metroid Prime 2, in my opinion, branches off too much and feels less "Metroidy" then the first Prime. The enviroments all look the same, and while the graphics are top-notch, the gameplay lacks a bit. Don't get me wrong.. it's a great game, but it doesn't meet the high expectations set by Metroid Prime;
Metroid 3 (thankfully) goes back to the Prime roots and feels Metroidy again.
(I left out Metroid Prime Hunters, because really, when it comes down to it, MPH isn't a Metroid game.)
My favorite 2D Metroid games was Metroid Fusion, and my favorite 3D Metroid game was Metroid Prime. (But may be taken over by Metroid Prime 3)
Hopefully you'll be able to make a desision based on my summaries..
Happy gaming! ;o