Didn't know it cost so much to put something on the Wii U Virtual Console that's on the Wii VC.
Front Mission I'm guessing there's some sort of a licensing issue.
I hope that's not the only thing you took away from that.
A lot of answers to questions like this usually boil down to money. It's all about the money.
If companies had all the money in the world, then you'd probably see so many things happen that you would not normally see.
In regards to Wii U virtual console. It could be for a variety of reasons. It could be that the game wouldn't make a profit so it's not worth spending the money to bring it over. It could be because of strategy reasons because releasing the game now wouldn't make as much money as it could later down the road. It could be because of the lack of resources and SE doesn't feel the need to add to that because it costs money, so they're playing the waiting game instead. If it's a licensing issue, then it's probably because someone isn't offering a lot of money or there are other deeper complications involved that's going to require even more money and it's just simply not worth it.
Should point out that a lot of Square Enix games on Wii virtual console haven't been released on Wii U virtual console in the west yet.