Same answer I'd give to any question like this: Play it in release order.

If you can't get into Metroid after an hour or so, move on to Super Metroid. 

I'd play the 2D ones in chronological order. Zero Mission (remake) /Metroid, Samus Returns (remake)/Metroid II, Super Metroid (Metroid III), Metroid Fusion (Metroid 4.) Play the prime series whenever you want, but if you are interested in its chronological position -- the Prime series takes place after Zero Mission/Metroid. 

Note: Super Metroid is the best of the 2D series, but Fusion is also very good in a different way. 

Don't bother with Other M, to be honest, unless you really enjoy the other games and want to try it. You can read the story details on Wiki after playing Super Metroid (the game takes place right after Super Metroid.) The game does some interesting things, but its not worth more than $20 (fortunately is only like $12 online.) Really don't bother with federation force. Prime Hunters has an okayish single player, but the highlight of that game back in the day was its multiplayer. It wouldn't hurt to skip it, but there is a character in the game that probably will be relevant to Metroid Prime 4. 

Other than that, enjoy! I wish I could play the best video game series ever for the first time again.  

Metroid Prime series takes place in between 1-2 but they are their own contained thing. Fusion is the last in Samus story.

Play Zero Mission first. It's a great remake of the NES game.

Then Play the Prime games including hunters.

Fed force takes place after Prime and well if you want to skip this game watch the last scene of it on YouTube AFTER you 100% Metroid Prime 3. MP3 has a true ending that needs to be seen.

Metroid II is next in the timeline.

Super Metroid.

Metroid Other M

Finally Metroid Fusion.

This is how the timeline goes in the series. If I were to recommend what games to play forgetting timeline. Zero Mission, Metroid Prime 1-3,Super Metroid and Metroid Fusion. Those are the best in the series.

I suggest starting with Super Metroid on the Snes and then Metroid Prime on the Gamecube straight after that. This will show you various things. First you'll recognise what all there is to love about Metroid. How the games open up, how they teach you stuff, how everything works. And you'll also recognize what a fucking fine job Retro studios did when they transported all these good things into 3D.

After these two masterpieces, you can elaborate further on the 2D or the 3D side of games either way. The other two Prime games are very good as well and should be played consequentually. While the first Metroid is a game that you should play if you really want to know the series' roots. It's very difficult and archaic. It goes to show why Super Metroid became the best game of all time. If you don't have the patience to go through the frst Metroid, pick up the GBA remake instead, Metroid Zero Mission.  Then you might want to play Metroid II on the Gameboy. Again, it's very difficult and archaic. Be patient.

What's left is Other M and Fusion. Play Other M first. It wants to tell too much story where it should rather just shut up and some design decisions are extremely stupid, but nevertheless it has quite some flair. Now you can play Fusion which is excellent.

If you like the series till now, you might even want to try that pinball game and Hunters on the DS.

You don't need Federation Force unless you are desparate for more Metroid in your life.

I prefer a timeline approach.

Metroid Zero Mission is the first one you should play. Chronologically, it's the first in the series, and it also has the best controls and is the best introduction to the series IMO.

The Prime series should be next. 1, Hunters, 2, 3 (has a true ending that needs to be unlocked when you 100% the game), Federation Force, in that order. Hunters is a bit disconnected from the other Prime games (it's also made by different developers and is regarded to be inferior to main 2 Primes), but one of the characters in it is looking like he'll be VERY important in Metroid Prime 4's plot. Federation Force's ending supports this even more, though I advise not playing Federation Force with the expectation of a true Metroid experience, since unfortunately it's not much like that, but the quick ending scene is very crucial to Metroid Prime 4's plot from the looks of things. If anything, I recommend looking into the game's gameplay to see if it interests you, otherwise I'd skip it and watch the ending on YouTube (it's the only thing that matters in the Prime plot in the grand scheme of things).

Next in the timeline is Metroid 2: Return of Samus, but this game is extremely dated, is low on exploration, and not super fun to play (unless you're looking for a challenge due to the limitations of the system, and not game design. It's not even in color!), so I'd advise to either wait for the 3DS remake (I'm sure you have enough to play until it releases ;) ), or you could play AM2R, a fan Metroid 2 remake that's extremely true to the series' core, and plays very much like Zero Mission. The only thing to note is that it's 2D Metroid for the pros, even the Easy difficulty needs a good bit of effort.

Super Metroid is next. This is regarded by most fans to be the ultimate 2D Metroid experience, though I honestly prefer Zero Mission and AM2R due to their tighter controls. It has very expansive exploring, and will put your skills to the test.

Other M is next in the timeline, but it's often criticized as you can tell. I think the game had amazing potential gameplay wise, but a lot of it is untrue to the series, but in a different way than the other black sheep of the franchise. It more has to do with Samus' characterization, but I don't want to get into it. I recommend trying it out if you got a copy nearby, but otherwise you're not missing out much, since the relevant plot details are mostly explained in Fusion.

Fusion is last in the timeline, and has been so for 15 years. It's my favorite in the series, and it plays similarly to Zero Mission. This game blends a somewhat more contrained approach to the exploration theme of the series, but it's still open enough to be enjoyable to series veterans. It also blends a good bit of story, which is why I really want a sequel T-T

For what it's worth, I'll mention Prime Pinball. It's a retelling of the original Prime in pinball format, make of that what you will :P

Hope this helps! I know I didn't include just the mainline ones, but I couldn't help it :P

If you want to play the least as possible, Zero Mission, Prime 1-3, Super Metroid and Fusion are the ones to play. They're the ones I played before I got hardcore into the series, and they're the ones I'd recommend to play to newcomers.

Thanks for the feedback guys. Also, are these games on Wii U virtual console?

I'd play the 2D ones in chronological order. Zero Mission (remake) /Metroid, Samus Returns (remake)/Metroid II, Super Metroid (Metroid III), Metroid Fusion (Metroid 4.) Play the prime series whenever you want, but if you are interested in its chronological position -- the Prime series takes place after Zero Mission/Metroid. 

Note: Super Metroid is the best of the 2D series, but Fusion is also very good in a different way. 

Don't bother with Other M, to be honest, unless you really enjoy the other games and want to try it. You can read the story details on Wiki after playing Super Metroid (the game takes place right after Super Metroid.) The game does some interesting things, but its not worth more than $20 (fortunately is only like $12 online.) Really don't bother with federation force. Prime Hunters has an okayish single player, but the highlight of that game back in the day was its multiplayer. It wouldn't hurt to skip it, but there is a character in the game that probably will be relevant to Metroid Prime 4. 

Other than that, enjoy! I wish I could play the best video game series ever for the first time again.