In all honesty, I don't see any fan games done in any style that fits GameFreak's, not well anyway. Reason being is that there's not really much resources in the way of 3D. However, I particularly like the games that manage to blend styles of DPP, HGSS & B&W to work together and have their own sort of game style. It's what I do, I try to take the best aspects of the DS games and make them blend into a nice consistent style. It's hard to pull off however.
But, if you're starting a new fan game, I recommend just working in an easy style with lots of resources until you're ready to move on and change your game's style. My recommendation would be to make it in RSE/FRLG style or go into HGSS, both of those have an abundance of resources, as does DPP. To do anything like Black and White, well, you'd be stuck for tiles and graphics and if you're working in RMXP, you'd have an issue to try and get the same possibilities.
But no matter what style you do, just keep it consistent. That's always been my motto. If you start mixing styles, your game wont work so well. So long as you can pull your game off in a style, then you'll be off to a flying start. But my favourite fan games are the ones that pull off their own style, and not just copying the style of gamefreak.