This one isn't hard. First off, stop treating the Virtual Console like new releases. When I look through the Virtual Console, I AM LOOKING TO SPEND MONEY. Limiting my selection is a HORRIBLE idea. So no more weekly releases, just GET IT ALL ON THERE WHENEVER POSSIBLE.
So everything that Nintendo has exclusive release rights on SHOULD BE ON THERE. If they want easy sorting, do it by popularity or reviews. This isn't difficult.
Trick number two is to link the potable and console Virtual Consoles. Get the platforms on each solidly downpact. If all you can get onto the 3DS is the Game Boy and NES, that's fine, but make it ARBITRARY to keep your purchases for each older system sync'd on demand between your 3DS and your Wii U. The game purchase, the current save, and the current "snapshot", should be synced up. This entire architecture needs to be seen as BOTH an easy profit vector and as a simple customer loyalty feature.
Moving your VC from the Wii to the Wii U shouldn't even by UNDER DISCUSSION. Hell, moving your entire VC library to the NEXT FIVE GENERATIONS OF NINTENDO HARDWARE should be a GIVEN. It's 2012 and you WANT people to believe that DRM WORKS, let alone that the virtual console will always be there for them. The VC is something that APPLE, MICROSOFT AND SONY WILL NEVER HAVE. So you really want people to feel like their Virtual Console purchases to feel just as real as the plastic cartridges of old.
In the end, the Virtual Console should almost be an awesome back-burner service, that just MAKES MONEY while you're busy making the big games. It NEEDS ITS OWN MAJOR PRODUCTION AND DEVELOPMENT STUDIO. When release schedules are slim (which Nintendo has dealt with steadily for FIFTEEN STRAIGHT YEARS), the story of someone meandering about the Virtual Console catalog and blowing $30-50 in a go 'cause of all that nostalgia should be COMMON. The idea that I can pick up some NES Mario and Zelda and play them at home, take my 3DS with me and have my games AS-IS outside shouldn't even be up for FUCKING DEBATE. They're all features that should ALREADY BE THERE (I'm sorry, I have a tendency to shout a lot in real life, as well).
TL:DR? Here's the bullet points:
- CATALOG AND FORGET. Put EVERYTHING you can on that service
- FOREVER OWNERSHIP. Guarantee that your VC library will always exist across Nintendo platforms
- PORTABLE GUARANTEE. Can you get it on both 3DS and Wii U? Then you HAVE BOTH, and if you want, we'll keep your game sync'd across both.
There's a lot of things Nintendo is ALREADY SQUANDERING before the Wii U even releases, but the Virtual Console is the most egregious.