There isn't much between them, but I will let others list of their virtues in detail.
One question though...you talk of their ability to last in a fight, using only stamina as a factor, but have chosen to remove defence from the equation. Why?
The ability to last in a fight is determined by both stamina and defence, and is usually listed as 'bulk' (a combo of both stamina and defence).
Is there a particular reason you wish to remove defence from the discussion?
One major difference I will point out is that Moltres has flying typing to consider, which gives it an edge in many of the meta relevant match ups that you would use a fire type for.
I would suggest that one reason that Flareon is considered a better choice is the availability of Flareon and candy to power up...most people would already have at least one Flareon if not an army - legendaries are not as readily available to all players equally.