What I find is rarely brought up is the fact that Jon Snow (assuming R+L=J), Dany and Aegon (assuming Targaryen blood) still have the capacity to go mad later in life (as the Mad King did). It can be triggered by anything. It seems to me that all the Targaryens are loose cannons, Viserys and Rhaegar included.
And then further down the line, any of their heirs with Targaryen blood will still have the same prospensity for madness whether they continue the incestuous tradition or not. (at least for a great number of generations)
This pretty much means that Stannis or one of the Baratheon bastards (likely Edric or Gendry) would be the best Kings. They have Targaryen blood in them, yes but it's been 'diluted' by Baratheon blood for one/two generations (which is a big deal), so the propensity for madness is far lower.
Edited by DamonPrinc3, 16 May 2013 - 05:51 AM.