Hmmm, to be honest it sounds to me like the game suffered from Ubisoft trying too hard. The problem with a female adventuring character like this in settings trying to be historical accurate is that they basically didn't happen, and the reaction it would get from the rest of the world wouldn't nessicarly be "fun". In trying to justify this and bring it to the forefront it seems like they had to get overcomplicated for the basics, and wound up writing themselves into a corner where if they explored it too deeply it would have fallen apart so it relied on generally vague definitions to cover things. I've run into similar problems before, especially with novels. There is a reason why you tend to see things mostly in fantasy or total alternative histories (Assasin's Creed is an Alternative History, but tries to keep things close to reality as part of it's appeal). Glossing over an unusually capable love interest or villainess is one thing due to limited screen time, a protaganist/more than a secondary character opens up whole new problems.
Overall from the sound of things it sounds to me like they should have dropped the whole "Assasin's Creed" title (which was done just for marketing) given that the connection to the series is tenative at best. If they had done this with a new, more "alternative" history setting (some kind of Steampunk variation or whatever) in the spirit of Assasin's Creed it might have worked better.
To be honest I always expected them to use a female protaganist at some point, but I kind of thought we'd see that if they ever got up to a more modern installement. I think it would work best if they ever did a 1920s or World War I game, as that's when you started to first see Women's Lib, it was new enough to explore the issues, and the so called "flappers" were everywhere. In say a World War I setting you could justify having a nurse or aide with relatively progressive attitudes who was actuall an Assasin sneaking off to kill the bad guys or whaetever a little more easily.
Don't misunderstand my overall point here, nothing against the female protaganist, it just seems like they tried to jam a bunch of stuff together that wasn't fully compadible within the liscence, and made a bit of a mess of things in trying to force it.
On a more contreversial note, I think one of Ubisoft's big problems is wanting to get away from the whole "traditional white hero" thing and try and turn the series into some kind of "we are the world" homage through Desmond's genetic memory (which doesn't include this paticular portable actually).
I plan to get AC III when I have some money, since I like the idea of it, but it's interesting to note that this is probably one of their biggest missteps ever. Recently I was just receiving a bit of a rant about the half native American protaganist in the game, oddly by a tribal member I'm vaguely aquainted with (remember I worked for 10 years at Indian casinos as security, and learned quite a bit about this myself). Starting with the unlikely Mohawk lineage, to the whole "use of a Tomahawk" as a weapon when actual East Coast Tribes fought largely with Warclubs, the Tomahawks largely being used as tools with what passed as their cutting edge just being too valuable and hard to repair to bounce off people's heads. You can club someone to death with a warclub (which is a bit more than just a piece of durrr caveman wood) just as easily, and still have your cutting implements which were harder to make and maintain for say chopping through trees. Later uses of axes and such for combat were apparently copied from settlers who carried hatchets and field axes for wilderness use. Now the western and mid-western tribes were a bit differant, but not anyone that would have been around during this period, the Mohawks apparently having a similar order of battle to the Mohegans and Mashentuckets, albiet being a bit less advanced than the Mohegans as the Mohegans were allies of the settlers and adapted from them a LOT quicker before some unfortunate land disputes which were sleazy on both sides. Somne of this I can verify from having visited the Museums down here. The basic point being that it seems for their attempts at diversity Ubisoft might have wanted to do more research.
Basically these (link is for the pictures) are what Connor's melee weapon of choice probably should have looked like:
http://www.ebay.com/sch/i.html?_nkw=indian+war+club
Just some general rambling because I'm bored, even if it's irrelevent to the initial post. For all I know though Connor DOES use a Warclub to fight with though, since as I said, it's hearsay so far from other rants I've heard.
In short I think Ubisoft is in such a rush to be differant, untraditional, and perhaps a bit contreversial in hero selection, that they don't really think things through, the latest portable game simply being their biggest mistake in trying to shoehorn so much "untraditional, yet historical" into one package for it's own sake and minimal research or planning.