I like the idea, though I’m not so sure about a couple things in their designs, particularly their cutie marks. Hiccup’s a viking, but I would expect him to have a talent related to building/repairing things and a cutie mark to reflect that. Dragon training is also a viable talent but he built that thing he caught Toothless with before he ever learned he was good with dragons and ponies seem to get their cutie marks at younger ages than he was when he met Toothless.  
Similarly, while night furies had a reputation as being the unholy offspring of lightning and death, Toothless is much friendlier than that and a skull and crossbones fits the reputation more than it fits how he actually is. I’m not entirely sure what kind of talent and cutie mark to suggest instead though, since he’s an animal with no particular job or special talent and a saddle cutie mark would seem inappropriate on a pony. Maybe a lightning bolt because of the lightning and death thing and being the fastest dragon, something similar to his breath weapon, or a shield representing how protective he is of others (particularly Hiccup)? I also think the tail and fins don’t really fit with the ponies in the show and being a batpony like Luna’s guards would suit him. Unless he’s supposed to be a dragon/pony hybrid (which could be entirely possible and half-dragons might not have cutie marks at all, so that could fix that issue) in which case you can leave him as he is.  
I hope I don’t sound too critical. I do actually like the idea of these characters being an alternate universe mane six and I don’t really have any other nitpicks about the set. The color schemes and elements of harmony suit all of them well and these two are the only ones I feel have cutie marks that don’t match.