Haha, kinda cool to see the name "Red Eyes" has taken a following.
So it's clearly a Heartless. It was the most likely answer for its' identity, though it would've been cooler to establish a mystery boss of something new, like Xemnas in KH FM and Lingering Sentiment in KH2 FM+.
If the Heartless have indeed already been in the Realm of Light by now (possibly during the Keyblade Wars)... then who THE HELL could make a Heartless that huge and deadly? Possibly the "general" of the Dark Keyblade Wielders during the Keyblade Wars? Maybe even the Heartless Master Xehanort could've spawned when he released his heart to take Terra's body?
Red Eyes bears many similarities to past bosses. His design evokes Xehanort's Guardian, the Dark Thorn in Beast's Castle, and somewhat of an Invisible and those... floating Dark Sphere things... the name escapes me, but they often appeared in Hollow Bastion and End of the World, and Aqua fights them in this Secret Episode too. Red Eyes is swift and attacks visciously like Cerberus (KH2) and the Living Bone Heartless from the Pride Lands (and their big brother the Groundshaker), and finally Maleficent's Dragon form. His multiple attack with different forms is reminescent of Xemnas' final fight with Sora and Riku.
I confess myself... dissapointed in the lack of importance the Secret Episode really played. It wasn't really the ultimate, dark, scare-the-shit-outta-me-Dark-Realm I'd expected after End of the World. I guess there's a lesson to not expect perfection, otherwise you'll just be dissapointed. It was, as said, just a preview for Bbs Volume Two - more time for Nomura to drag his ass to make KHIII. Just when 3D is coming, and it sounds like it was gonna tie up most of the plot threads and lead into the big KHIII... darn. :\