It's worth noting that Meru was a Wingly and a full Dragoon. It's possible Winglies just can't access the Divine Dragoon Spirit for whatever reason; the lore in the game isn't really very complete, so there's a lot of room to invent your own mythology. Of a certainty, a known god made a tree to produce 108 forms of life and the 108th was meant to "reset" the world. We know nothing else about this god, its character, or whether it had any greater plans beyond its reset cycle - might be interesting for the plot of the game to explore, maybe set after the original - God returns, things get messed up - whatever. There are unanswered questions about a lot of things, like what the Divine Dragon and its spirit actually are or represent; the Winglies presumably chained it down, but why didn't the humans release it after the war, considering their alliance with dragons?
Anyway, the only Wingly who tries that we know off can't bond to the Divine Dragoon Spirit. Maybe it's him, maybe it's a racial thing, who knows. Meru and Lenus manage okay with a regular Dragoon Spirit.
Freeform works okay for me. FATE's free and could work for something like this with a little work to get a subsystem going (the shape of it's easy enough to predict, every turn as a Dragoon does stress to a special track, Dragoon form having a special Refresh to reflect its growth...) but, you know, different strokes and all. I'd be willing to help out with mechanical design if you did want to run it in FATE.