From talking with people involved with Madden NFL Football at the 3DS launch, it was very much a rush job. Basically, they were given a deadline, and they had to do what they could do in that time. Unfortunately, that meant a solid framework of a game with no depth.
I'd also assume that development on a future 3DS Madden game was halted until production on Madden NFL 13 for all consoles began, which likely gave them time to look at sales and nix the 3DS version of Madden 13. Basically, this was a business decision that we can all poke holes in (The prior game was a lackluster effort. 3DS didn't pick up steam until the fall. etc.)
The weird thing about all this is that I was under the assumption that the Wii version sold like crap, but I'm guessing it's not doing that bad if they're making another one.
Side note: I'm willing to fight anyone (not with words, but with fists) who wants to look me in the eyes (likely impossible given we're on the internet) and tell me that the Wii version doesn't receive any effort. Does it get nearly as much love as the HD versions? Hell no (it also doesn't sell as much). Does it basically have the equivalent of a B team working on it? Probably.
I've made mention of the fact that I see Madden on Wii as an excellent B-movie of a game. It's got warts (the quality of the visuals has stagnated since the smooth 2009 redesign, for one), but I enjoy the hell out of it. For me, it is like someone at EA was like "Hey, that one guy really liked Madden back in the early '00s, but fell off the wagon when it got more complicated. Let's make a game just for him!" I love Madden on Wii.