.

There will be retail fees, actually. In order not to infuriate retailers (Nintendo needs them to sell the console) Nintendo came up with a way to give them a share - the downloadable games will be paid for in stores, you just get a download code or something.

And even if there is another way and if the process is cheaper (which it might be and it also might not be, since the whole game download service costs something as well) the experience from other services (Steam...) tells us that games are almost never cheaper in downloadable form, unless you wait for some sort of sale.

i cant agree with you more

the games should be cheaper but looking at the 3DS pricing model they probably won't.  even vita (which is cheaper than msrp) isn't cheaper by much (~5-10%) and typically store sales will beat its downloadable pricing.  on vita i'll pay the extra money and write it off as a "convinence charge for not having to fuck around with carts on the go" fee.  for a home console i'm not willing to pay that "fee".

Should they be? Certainly. 

Will they be? No.

Manufacturers need to work with retail stores, it gives them space on the shelf, therefore I doubt that these companies will ever try and undercut their retail partners, so eShop and any other will have a price almost identical to what the retail store has (the MSRP)