Sales of the 3DS have already gotten a big increase since the price drop, and that will help with developer support (plenty of companies already pledged support, just waiting for those games to come out).
Sony and Microsoft have the final say for prices on their digital services (well, I think Indy games on Xbox 360 aren't), so I don't see Nintendo doing any different. Maybe let publishers release free demos.
No digital game, free or not, will get any significant amount of people to buy a system. You might get a tiny amount (like a few dozen or few hundred), but not enough to make any impact on sales numbers.
Retro Studios is a pretty small developer (about 60 total employees), so not sure it would be a good idea for them to divert time and resources to making eShop games (especially several at a time) instead of focusing on retail games. I think they could maybe make a small game on the side.