You're missing my point with transfers. See, if I were to buy a new PS3, I would just deactivate my account on the current used PS3, sell the used PS3, and then I could donwload everything on my account on my new PS3.
With the 3DS I can do a system transfer, but I need both DS' for that to work. Which means I can't sell my current, soon-to-be obsolete 3DS without losing everything I bought online. Sure, I can transfer it, assuming I keep this 3DS, but I can't recoup some of my spent money until after the transfer.
Personally it's not a big deal to me. I haven't bought anything off the eshop specifically because of this reason, but it does affect other 3DS owners.