Funny thing is, they've pretty much done that very thing in the past. I remember in Maximum Carnage on the Genesis and SNES, the end of the first stage actually dictates that Spider-Man get his ass kicked, all for the progression of the story. So no matter how well you play, there's no way to actually win at that part.
I feel like I've seen it elsewhere too, probably during the 16-bit era again, but I can't remember where exactly.
To be fair in Ezio's case though, he was a total ruffian before donning the hood. He was a playboy, sure, but he was also essentially the leader of a street gang, which would likely give him at least some experience in combat (not to mention his father being an Assassin himself, so you never know if he maybe had some amount of fencing practice in the past). Plus it's understood that, in the case of Ezio and Connor both, their actions during gameplay are being controlled by Desmond, so naturally they'll come across as being more skilled than they likely would have been if the story were strictly about them.
And in Far Cry 3, if you've ever read anything from the writer, it's intended in kind of an artsy-fartsy way that the player is actually a "character" in the game, and that they're the main reason why combat comes so naturally to Jason.
Still, those are all just excuses. I agree that if a story is about someone's beginnings, there should be some failings along the way. It's only natural. The gameplay should jibe with the character.