Publishers can already have digital SKUs be cheaper than their retail copies. We've already seen that a bit in Japan.
And there's already a lot of flexibility. Publishers can set the price of 3DS games to whatever the hell they want. Even NoA has been doing this for about a year now. Most recent cases are that Disney game and Mario Golf: World Tour at $29.99 and the new Kirby being what, $35? Big titles can get away with $39.99, but most titles should be a bit cheaper, and Nintendo does seem to be finally realizing that kind of.
EDIT: Basically, publishers are choosing to price their games at prices that are sometimes higher than what a lot of people are willing to pay for it. It's a serious issue.
I suppose one of the reasons for the retail prices are also costs of producing carts / discs. IIRC, Nirolak said the cost if 12$ per cart, or something like that, and that has an effect on the final cost to the customer. Right now, it's possible the prices went down, and that's why we're seeing Nintendo reducing prices of older titles (even more recent ones) and also things like Mario Golf at 29.99. Of course, it's also a recent Nintendo's change of policy, seeing how they also permanently lowered W101, Ninja Gaiden and G&W digital prices, and how NoE is using VC games as bonuses for those who buy digital SKUs of games (in the Mario Kart case, we have something similar to a preorder, basically: put down a part of the money, then pay the rest when the good arrives).
And it's true that, in Japan, this is already happening. It needs also to be said that, IIRC, retailers can sell games at slightly discounted prices, and Amazon always does that, with 18-20% discounts, so it's also the market being more used at discounted prices at launch, but the number of games with at least 500 Yen discounts is increasing. The last Nobunaga's Ambition was 1,200 Yen lower on PSN (starting from 8,800 Yen, though... :lol ), but recently Theatrhythm left me legit shook: 6,200 Yen retail, 4,800 on eShop. Yep, that's a 1,400 discount on eShop, and it beats also Amazon :O
Download cards = no carts production costs, much lowered inventory costs for retailers, so, in theory, both parties should seriously think about it.
Having digital codes on shelves means also having some digital titles (those from main sh, not indies) on shelves right at the side of their possible retail SKUs , which would mean bigger presence and bigger diversity in the eyes of not-experienced customers, who don't know the digital offering of the system(s)
They should also think about a system where the retailer could actually produce download cards by itself, thanks to a special printer + private online service that lets you buy stocks of digital codes and then you simply print the codes on the special card and...you can restock them whenever you need, in the exact quantity you need, easily. Heck, if indie devs get involved, that would mean having indie titles on shelves too, in theory.
Ok, the last part was certainly less related with things that can happen in the next few years (hopefully, not, but still...); however, yeah, publishers and retailers need to talk about the possibility seriously.