In a personal theory, it is because Nintendo saw that people were downloading ROMs on the Internet and felt maybe it would be a good way to cash in the opportunity and can you blame them? This item is also designed to some degree to attract more retro gamers and I believe it has done just that. Keep in mind what I'm going to do is pick out a list of games I believe would make great additions to the Virtual Console and tell you why I believe that to be the case.
NES
Double Dragon 2
The sequel to Double Dragon would be a perfect fit to the franchise. It's a classic beat "em up game that you could play for hours and not get bored. It had some pretty good cut scenes but what won it was the game play. The first one was good but this one actually improved it and should get on there without question. You had a good challenge ahead of you.
TMNT 3
You got the first two Turtles games on the Virtual Console and also Turtles in Time as well. Why not this one? It was actually pretty fun to play and everything was so responsive and the difficultly was there and just naturally harder. The story was told and you had some first time villains on there such as Ground Chuck, Dirtbag, I believe Tokka and Rahzer made their first appearance along with from the Ninja Turtles Movie Secret of the Ooze Super Shredder. It was overall fun.
Castlevania 3
It"s one of the Castlevania games so it has to get on there without introduction. It is a crime that this game isn't on there yet and I'm not sure when that's going to happen. What made this game cool was it had alternate paths to get to the end and you meet three characters. This marked the first appearance I can recall seeing Alucard. Multiple endings depending on who you have or don't have teaming up with you. It holds the greatness of the first Castlevania game and would be a great game to the ever-growing Virtual Console library.
Mega Man 3-6
Insert any Mega Man NES game and this would work just fine. Sure, the game play was pretty much the same but it doesn't take away the enjoyment factor. I know Mega Man is a franchise that is considered stale and that's all opinion but we're talking about the classic Mega Man games. Knowing full well that they are on the Mega Man Anniversary Collection is fine, but I'm talking about for the Virtual Console itself. If you can put the first two Mega Man games on there, why not the rest and go all the way? They are fun and have some challenges and personally I think Mega Man 4 is the easiest of the bunch.
SNES
Super Mario All Stars
Money can be made with adding this to the addition. Sure, it's a collection of games that were remade but why not. It has them enhanced in terms of the look and plus you can save your progress. There are two different versions, one with Super Mario World and the other without. You could put either or in there and it would work just fine.
Mega Man X-X3
You could put them on the Virtual Console and it'd be a hit to download. This series took another step and went into a little darker area with Reploids and Mavericks. The game play was like the classic Mega Man games except it had armor pieces and also brought in the introduction to Zero. In this series you were introduced to an intro stage before going into picking the Maverick you wanted to destroy. Those are available in the Mega Man X Collection but why not add it here as well.
N64
Legend of Zelda: Majora's Mask
You got the first two Zelda games on there along with A Link to the Past and the Ocarina of Time. How about complete the cycle and add this one to the mix? This one is different from the others mainly because of the storyline and using the time limit as a way of telling it.
Mega Man 64/Legends
At first I was a bit unsure on the game itself making a transition to the 3D world but then I actually played it and have to admit it wasn't that bad. It's a series that ended way too short but I'll talk about Mega Man another time directly.
Genesis
Castlevania Bloodlines
This is a Castlevania game and the expectations are that it's supposed to be great and this is one of the best Castlevania games that I have ever personally played. You can pick two characters and can have the difficulty altered. It holds to the tradition of the original Castlevania games other than the option of just picking one character and sticking them to the end.
I'm not sure on the time frame but I don't see them involved with the Virtual Console. If these aren't involved, it's a crime. Give it time I suppose but if you're wondering why didn't I mention the TurboGrafix, Neo Geo, and Sega Master games in the mix. Mainly because of never owning the systems and not being overly familiar with the game library. These are games I'd like to see get on the Virtual Console as the primary ones. Anything else would be a bonus.