I suspect the problem is that they were struggling to get games out on Wii U (and even 3DS) and had to put the VC on the back burner.
The VC development part of Nintendo is not big, maybe between 2-3 small teams I'd guess. Most of the VC development wasn't Nintendo it was Hudson on TG16, Sega on Master System and Genesis, D4 Enterprise on NeoGeo, and some other spread between other systems and arcade.
Here's what likely happened:
Late 2010 - Nintendo releases final Wii VC games, starts on 3DS VC
Mid 2011 - Nintendo finishes GB and GBC support, starts on NES, GBA
Q3 2011 - Nintendo get NES and GBA betas for Ambassadors
Early 2012 - Nintendo finishes work on NES, GBA not going as well as planned
Q2 2012 - Teams start ramping up Wii U VC
Q1 2013 - Early games done, issues linger
Q2 2013 - Finish NES, SNES, move on to GBA, N64 and DS (probably others)
Q4 2013 - Get prototype of DS games working
Q2 2014 - Finishes GBA games
As the system get more complex they take more time also they continue to support systems that have already released with updates to working game lists. I also think that there are other things they are working on, I'd suspect they are actively attempting GCN even if it never happens.
I think the breadth of VC simply started outpacing the team. It's very clear they have been focusing on certain things and moving in a relatively linear fashion from new project to project. Still, the overall volume is highly dependent on 3rd parties. Konami doesn't seem to give quite the same shit as Hudson and that may continue to dampen release lineups. Sega too.