factors I would consider:
* BbS launched almost right after new years. Younger kids have the most disposable income at this time period, making purchases easier. There were also no serious games for the PSP launching at the same time vying for users' mindshare. KI launched a week prior for 3DS, and while not a real series title, the marketing blitz Nintendo's provided likely resulted in some cannibalized sales.
* DS/PSP userbase at time of release. It does take a serious fan to buy a system for a game.
* Number of previous SquareEnix games/RPGs/etc prior to release. This is the big one IMO, Square's obviously shown they're ramping up support for 3DS but we've only seen the start of things. Only thing 3DS has had Square-wise so far is Theatrhythm, which has the looks of a cash-in if you don't have access to the demo. Both DS and PSP releases came after waves of SE titles, and that's a userbase that may not necessarily buy a system for KH, but will buy KH if they already owned the system.
Numbers could have been a lot better but I wouldn't say it's at bomba range. I'd be interested to see how SE follows up over the years though; maybe I'm wrong here but Nomura-ish titles like Dissidia and Crisis Core share a similar userbase with KH, and if they don't end up migrating those types of titles to the 3DS at a later date then this KH3D launch would have been a complete waste. Like many people in the thread have said it would have sold double on the PSP easy. It'd be like Capcom making MH3G and then going back to PSP/Vita for MH4P.