I don't think Connor's not exemplifying the views of the assassins was poor character development. I think this is an actual exploration by the developers into the cause. He's meant to not think what his actions really mean. He's meant to have an inner conflict over who he should be helping, what will result in the better outcome, between ideals and reality. The Templars are also meant to be sympathetic. They all exemplify a different aspect of the Templar ideology, and some of those make you legitimately question Connor's actions. Maybe I'm alone in this, but I find AC3 more ideologically challenging than either of the other two. AC2-era probably had the largest share of Templars who were just dicks and needed to die, and the fight against oppression and the motive of revenge were both apparent. In AC3 there's a bit of confusion over who wants what, Haytham in particular makes a good point about how the Patriots are using Connor and don't necessarily uphold Connor's ideals or those of the assassins. Even in gameplay, patriots are just as ready to give you a shove with their rifle as any British soldier, and you don't even feel welcome in the forts that you liberate. AC3 is about questioning what and who is right, and whether either side's ideal state could ever be achieved.
That said, the Illuminati or Freemasons. Shady force controlling things behind the scenes, no-one's sure what they really do? Come on. Although, they seem to already have established the Templars as being in every nook and cranny of control.