Alright, so I've recently fallen in love with fighting games (thanks to MvC 3 and MK) and I was wondering which version of this game I should play first?

" MvC 3 and MK, console version best experience of the game"

3ds SSFIV is not great...
I mean it's fun to play casually, but the controls are very bad imo, the d-pad is not that good and the placement of all the buttons make it awkward to play for a long time.

I bought it together with  my 3DS at launch and havent played a lot of it.

That being said, I own SSFIV for consoles and THAT is a great game, I have played several hundreds of hours and still am not tired of it and just have to keep playing it.
So I would say go for the console version.

I'd have to say the 3DS version first, mainly because the online community there is a lot less likely to crush your soul and ego at the same time. You'll have a fun on-the-go fighter for your handheld which is ideal, seeing as the bigger games are still underway. Then if you really like it, you can eventually add it to your console collection.