I have a fun and facinating little solution to this if they continue to build the emulator into the ROM...
how about lifting policies on modifying code on these games? they dipped their baby toes into this with things like 3D Classics Kid Icarus having far better controls based on the Game Boy title, or letting Sega make enhanced emulators for their titles, or some of the ideas like Super Luigi Bros. or Fast Mario Bros. in the NES Remix packages? this could allow for a number of things.
-LUA scripts like what's possible with FCEUX. There's a LUA script for Metroid that pretty much adds in the mini-map and the pause menus from Super Metroid, including quick switch between ice beam and wave beam after they've been aquired and it makes the game SO much more playable...! they could of course run with it in other directions too, like say... right analog quick aim of eggs in Super Mario Advance 3, or bullet hell Super Mario World, or Power-up boxes ala' Mario Kart in F-Zero...! just fun, Game Genie-Esque scripting things that can be toggled around. this also could be used to have... y'know, had a toggle to make Mysterious Murasame Castle a proper 'NES' game (English title, replaced shogi piece powerups with chess piece sprites, MMC1 style music emulation instead of the FDS Sounding music)
-Private reach-out strategies to work out a small recognition deals with folks that made popular fan mods to have their mods toggle-able on some emulated games. This could be huge. I'm not just talking Kaizo Mario world and Rockman 4 MI (ZING! My thread about that game is lonely...) or stuff like that. I'm talking about huge stuff like cleaning up Mother 3 Fan Translation for an ESRB rating, or maybe getting something akin to Sega's relationship with Christian "Taxman" Whitehead going with fans who are willing to do these reverse engineering jobs in exchange for working on the inside just a bit and getting industry experience they could use in the future! (For those out of the loop, The Taxman in 2008 made an engine for iOS specifically designed to run proper updated, but slavishly close to the original ports of Sonic games, and Sega ended up hiring him on and licencing his engine to make the 2010 remake of Sonic CD that had playable Tails, choosable soundtrack, sonic 2 style spindash and Sonic CD style spindash togglable, many of the terrain clipping bugs fixed, and proper 16:9 support in it. He also did a Sonic 1 and Sonic 2 port to iOS with Sonic 3 style stuff added in like playable tails and knux, spin dash, 7 emeralds, a recreated Hidden Palace zone complete with a new Dr. Robotnik boss battle involving a trombone, as well as other extra goodies)
- allocation of some Treehouse resources or licencing to 8-4 Play to localization efforts similar to how Sega was allowed to release localized Monster World IV to VC. It's not necessarily Mother 3 that I'm thinking of here either. Now that Mysterious Murasame Castle has made it over, I feel it's time for the other two big lost FDS series to emerge and come into the limelight. I feel the world is ready for stuff like Shin Onigashima and the Famicom Detective Club games. Or the various Fire Emblem stuff. Or For the Frog the Bell Tolls. Or the original X. I feel in particular the Gameboy games I just mentioned could easily have enough push put behind them to drum up interest to recoup the small effort...!
- Satellaview Virtual Console. If we're going to string all the above ideas together, then this would probably be the ultimate result, and something I think has the potential to be especially exciting, although it'd take a good deal of re-engineering with modern internet tools, such as some sort of streamed audio for stuff like the BS Zelda titles, as well as leaderboard and potential social media intigration, as Satellaview VC would be a venture into Nintendo putting out a subscription based service. possibly with original content too. and they could try their hand at a free VC game of the month with this subscription. like... providing you with a copy of Alleyway or Urban Champion for your hard earned cash.