First off, there's the tool itself. Although the Pikmin animation that runs on your Nintendo 3DS during the transfer is amusing, it seems like a rush job. During my attempts to transfer select titles from my DSi to my 3DS, I encountered plenty of problems. The tool kept chiming out mid-way because it was unable to connect to the Internet even though there were no actual problems with my wireless. And because of that, copying over all the games I wanted turned out to be a long and tedious process (one that I still haven't fully completed). Eventually I was able to consistently choose titles one after the other with few error screens in between, but that was only after having gone through all those regular interruptions. Because I own over 100 downloadable titles, you must be wondering, "Why not just do the Full Transfer?" And this leads me to my next point.
One other area where Nintendo has really dropped the ball is in the matter of leftover Nintendo Points. It's one thing to prohibit the use of unused Nintendo Points cards on the new eShop platform. That I somewhat get. But I don't understand why you can't bring over any remaining points you have sitting around on the DSi Shop and convert them to eShop cash.
Unfortunately, after I brought over some of my DSiWare games to the 3DS, the disappointments only continued. Not only are you unable to assign any DSiWare games as your 'Favourite Title' in the Friends List menu, but Nintendo has also disabled use of the Home Menu whilst playing. Would it have been so hard to implement these features? They seem little, but they do go a long way -- at least, in my overall experience with the system. Especially with the latter, players wouldn't have felt a loss in interaction with the 3DS platform now that they're playing games that were designed with the DSi in mind. Instead, the inability to access the Home Menu during play ultimately contradicts the very strategy of player immersion that Nintendo has been pushing again and again.
Also, you'll notice that some games actually have smaller block sizes on the 3DS than they did on the DSi, which does allow you to hold more games on your menu screen. But I still find myself feeling disappointed that the internal memory doesn't give you more leeway to house more DSiWare releases. Allowing players to run games off the SD Card would have been a simple fix for this problem, but once again, Nintendo didn't take up this opportunity. I figured they would have cracked down on this by now (especially with the numerous complaints people made with the DSi), so that's what makes this even more upsetting.
Nintendo did get a few things right with the DSiWare transfer system, though. Thankfully, these games do count as entries for your Activity Log and you are able to rate them on the eShop after spending at least an hour with them. So there's a positive there. But as a whole, I'm still very disappointed with how Nintendo has handled this whole thing. Instead of being worth the wait, the System Transfer feature has just made me feel like Nintendo has neglected my needs as a gamer and as a future customer and I'm not happy about that at all.