There is a technical reason: storage space. Making a couple of models for important characters is one thing, making different models for a couple of dozen creatures that basically come down to canon fodder is something else.
They could make high quality pokemodels because it was a download, so storage space isn't (for the creators at least) an issue, that's all up to how much space you have left on your 3DS.
If I had to choose between making a couple of models for minor "characters" or more content in another area, I'd go for the latter.
Actually, I'm not sure storage space would be an issue. Textures could be re-used across the HQ and LQ models for Dream Eaters, since they seem to be high enough quality as is in the Wondernyan screen to hold up even when they're taking up most of the screen (which makes sense; with the 3DS's RAM, a single 512x512 or 512x256 texture map to replace KH2's single 256x256 map would be entirely reasonable in gameplay, especially since KH doesn't use bump/normal maps, and that's plenty big for a 400x240 screen given KH's tendency towards large areas of bold color without much intricate detail). The only thing they'd really need to change is the polygonal model itself, and those are fairly small if the XNALara downloads I found are anything to go by (Aqua is 250KB for a ~3k poly model, KH2 Riku is 370KB for a ~5k poly model). Given the lack of small separate details and the 3DS's screen size, 10k should be plenty to make a Dream Eater look nice and smooth while retaining mesh file sizes under 1MB -- there's about 50 Dream Eaters, so you'd be looking at less than 50MB of extra space, which is, quite honestly, nothing on a 4GB card unless they're filled to the last byte.
As far as I can tell, they should have plenty of extra space, so that shouldn't be an issue. Kingdom Hearts II only took up one side of a CD (3.7GB), and that's with three CG videos at 640x480 (at the very most, we'll get three CG vids at 800x240, which is 5/8ths of the PS2's resolution, and almost certainly has some neat compression tricks that make the size relatively lower for the resolution due to the repetition inherent in 3D... and I kind of doubt we're getting three CG vids, given that Birth by Sleep only had one and the pre-rendered in-engine Secret Ending; IIRC, KH2 had one pre-rendered in-engine cutscene as well, which would probably be unnecessary in 3D since it's using a cart). KH2 also had an incredible 10 hours of voiced cutscenes as well, compared to maybe 4 1/2 for Birth by Sleep, and sound is relatively space-intensive, which should free up even more space. KHII had higher-poly models too, though I'm not sure how much that affects the overall size.
The only thing that should increase in size from KH2 is textures, which should be larger, higher-res files to take advantage of the 3DS's 3x increase in RAM. Those will almost certainly be more limited by RAM than by disc space, however, since textures don't appear to make up a majority of the data anyway -- every player, ally, NPC, enemy and boss (with gameplay animations), animation-less HQ cutscene model, and static item in KH2 put together weighs in at a bit over 700MB; even if the world data doubles that, halving the sound and video requirements should allow texture data to be tripled without much of an issue given that the mesh size would decrease.
By the way, Pokedex 3D? It's 23MB (179 blocks) total, and I'm pretty sure it downloads all of the Pokemon at once rather than taking more blocks when you find new ones. If they can't make room for 23MB in a 4GB game with nearly-imperceptible sound/video compression tweaks, something's gone wrong (and we'd probably end up with FFXII-quality sound =X ).
