Nobody (outside of Nintendo) seems to know, but there sure is a lot of conjecture. On the technical side, the top screen should be able to play games that use the SNES's lower resolutions without scaling. I've only found this this vague official statement from Satoru Iwata:
While Wii U and Nintendo 3DS already offer Virtual Console software, I feel that we have not been able to take full advantage of our assets yet, so we would like to enrich our Virtual Console lineup.
The SNES isn't the only classic system conspicuous for its absence from the 3DS Virtual Console. GBA would seem to be a perfect fit (it's been announced as "coming soon" for the WiiU along with N64), as well as the Virtual Boy. We've got Game Gear, but no Master System (although it is on Wii). Even the systems that are represented have only seen a trickle of games released on Virtual Console.
My theory? Nintendo is intentionally keeping the "supply" low to keep demand high. If they were to "flood the market" by making the entire back catalog of the supported systems available at once, it would be harder to get attention for new releases. So it makes sense that they would only release a few carefully selected feature games at a time. Withholding the Virtual Console releases could also help increase visibility for the "3D Classics" on 3DS and HD remakes of N64/GameCube games on the WiiU.
GBC,GBA,GBA SP,NDS,NGPC,Panasonic FZ-10 3DO,NES,Sega Nomad,Sega CDX w/Power Base Converter,PS1,PS2,PS3,Saturn,Dreamcast,PC (Win 98, XP, 7),Dingoo A320,Dingoo A330,Gemei A330,LetCool N350JP,PAP-GAMETA,GCW-Zero SE,Kyocera Rise,2DS,GP2X-F100,GPD G7,JXD 100,JXD A1000,JXD A3300,JXD F3000,JXD V5000,JXD S7300B,Hyperkin SupaBoy
Currently playing: Theatrhythm Final Fantasy Curtain Call (2DS)