Word coming out of Nintendo of Japan that when the DSiWare transfer program hits the 3DS during E3 you might have something more to consider when deciding whether or not to keep your DSiWare games on your original DSi/XL or move them to your new 3DS. It seems that the transfer software will annihilate your save files for those games.
The save games for DSiWare are bundled with the game, and it seems, perhaps due to an exploit in some of the more poorly coded games, that Nintendo is doing this to prevent any possible exploits from pervading the 3DS system.
This doesn’t seem like the biggest deal to me, as most DSiWare games aren’t exactly grand adventures, but more often smaller games where the replay value could actually be improved by a game save wipe, but for those who care you might want to keep this in mind when making the decision to transfer your games, or keep them on the original system.
A wonderful side note however is that you can apparently choose to transfer any game you want from one system to another, and leave the ones you choose on your DSi, you can even transfer games from multiple DSi’s and DSi XL’s to the same 3DS, so the truly hardcore DSiWare fans will have the opportunity to mix and match.
Oh, and of course you can’t transfer games from your 3DS back to your DSi, but you should not have expected that anyway.