Firstly: I will admit that I prefer FATE.
I am confused, however, as to what aspects of the Pathfinder system we would use if not the combat system. The skill system in pathfinder is explicitly based on the combat class each player selects, with certain choices being strictly better than others. I'm also not clear on how the two would be meshed. Combat abilities are skills, in Fate, whereas in Pathfinder, they're a function of your species and profession.
And the skill pyramid, while hard to justify in-setting, is a relatively simple method to encourage healthy play. In truth, success in system-based games, as with freeform games, are largely based on GM fiat. If, in the hypothetical absence of a skill pyramid, you were to spend 10 points on your fighting skill of choice, the GM would simply make opponents have the same skill level or somewhat lower or higher, depending on what they decided your odds of success should be. Spending those 10 points only pigeonholes your character and makes creating party-appropriate antagonists more difficult.
As for the difficulty of character creation, I will simply have to disagree with you here. Particularly for the Fate Core as it exists in its current version, you are allowed to select three of your 5 aspects: your High Concept (who/what you are), your Trouble (what aspect of your character repeatedly creates problems for yourself or the group), and then your history aspect. The other two aspects you collaborate with one other player to see how your characters would interact, and turn that into an aspect as well. This gets around the "Well, we're collectively an unusually short, warhammer-toting, human mercenary, an elvish flutist, and a gnome astronomer. How did we get together as a group, again?" that can easily develop in games that don't have collaborative character creation. To me, the pre-existing interpersonal connections makes for much smoother gameplay, as it reduces the risk of genuinely incompatible characters.
I think, as Robyn stated, some of the difficulties here stem from the fact that we're looking at two different editions. The Fate Core has a mere 18 skills (though I can add more if I think they'll become necessary), as well as fairly coherent rules for what you can or can't do with stunts. Robyn's character is also using some material from the magic systems supplement. If people are averse to buying into the Kickstarter, I can share the Core, as well as the particular magic system I'm planning on using, as doing so is discouraged rather than explicitly disallowed. I will need a way to directly contact anyone who wants a copy, however, as it's a fairly large PDF.