Board Thread:Series general discussion/@comment-5415330-20170420110400/@comment-2112031-20170421000824
I never really got the impression that they idealized the catholic monarchs. Aside from the fact that they're barely in the movie, what little we see of them doesn't really paint either a positive or negative picture. The fact that the Templars manipulated Isabella through her faith is, as Sol Pacificus mentioned, not really an indication that she would have sided with them.
As for Prince Ahmed, I suppose the Assassins could have covertly retrieved him from the Spanish Army and then the Templars, under the guise of the Inquisition, went to retrieve him in order to exchange him for the Apple. From the perspective of the monarchs and the army, the inquisitors were just doing their job by retrieving the prince.
Speaking of the Assassins, we have to keep in mind that Aguilar was the last remaining member of the Assassins Guild in Granada. It's pretty likely that he spent the following years trying to rebuild a guild in Granada, probably with help from the other guilds. It seems that, as Sol Pacificus mentioned, the Spanish Brotherhood was united under the leadership of the main guild, located in Madrid, by the time of Brotherhood.
Interestingly enough, despite the stereotype of the Assassins supposedly being anti-establishment anarchists, they're really not. Ideally, the Assassins believe that the leaders should reflect the will of the people and take care of them, rather than abuse their power for personal gain. As Ezio told Cesare: "a true leader empowers the people he rules".
The Assassins supported and cooperated with plenty of rulers and authority figures throughout history. Although some of these alliances are indeed questionable, such as the Medici, one could argue that they were better than the alternatives. We also know of at least one Assassin, Yolande of Aragon, who was both a monarch and a Mentor. So we know of at least one occasion when the Assassins were in a direct leadership position, kinda makes you wonder how it went.
As for Sun Yat-sen, I agree that it seems like a missed opportunity to do somthing better with him. I don't really mind him being a Templar, but I do think it would have been better if we had actually seen what had happened to him, rather than just being told. Perhaps it could later be revealed that he was trying to make peace and even forge an alliance with the Assassins, and then one of his fellow Templars killed him in an effort to prevent that, not unlike Bellec killing Mirabeau.
After all, it was stated that the Templars in China had fractured into multiple factions, with the Shanghai Rite struggling to control the others. It's not too difficult to imagine that a Templar from one of the other factions might have believed that the fallout from Sun Yat-sen's death would have preferable to having a possible alliance with the Assassins.