I would have expected 2.5's development to go a lot faster than 1.5's since they didn't have to start from scratch this time.
Doesn't Re:CoM use the later version of the engine from KH2? Yeah.
However, KH2FM's got a lot more content (and therefore more need for testing) than KH1FM had. And probably more of a need for memory-intensive optimization (remember that the Lingering Will has a *ton* of attacks, there are the reaction commands, the Drive Forms (though the game's happy to have load times for those, IIRC), and some other stuff. Things like the 1000-Heartless battle might need some work to look good in HD, too - that stuff used a LOT of little tricks and sleight of hand that might not look nearly as good in higher resolution.
Also, don't forget that BBSFM's got some stuff that'll take additional work, too - specifically, the Mirage Arena. I strongly doubt that KH 2.5 HD Remix is going to have multiplayer in it, so that means restructuring the Mirage Arena somewhat (removing group-heal abilities, removing stuff like the Confetti ability, possibly removing the redundant-without-multiplayer Mirage Arena versions of Command Board and Rumble racing, and rebalancing some of the rewards/costs of what remains accordingly). It also means that they could make it possible to actually play as Aqua, Ventus, or Terra, and not just the Mirage forms of each (since the idea behind that was to prevent you from having two Terras onscreen, for example).