I’ve gotten a couple questions on this, and it seems that there may be some confusion, so I figured I’d ramble a bit just in the hopes of clarifying things.
Ares is designed to be a fully flexible framework where you can build whatever game you want. Of course, the further afield you go from what’s already built, the more work it will be for you. Think of it like a house you’ve just bought. You can:
- Put up some curtains and furniture (basic configuration)
- Remodel the bathroom and change the countertops (minor code tweaks), or
- Start knocking down walls and gutting the place (ripping out or extensively modifying core systems).
It’s your house; do what you want. I will support you within reason (even if I don’t like the changes you’re making), but I am not a construction company here to make a house that works for everybody “out of the box”. Even if that were possible, it would be way too much work. 
FS3, on the other hand, is my personal pet skill system. It’s right there in the name-- Faraday’s Simple Skill System (FS3). It works the way I want it to work. It’s customizable to an extent (skill lists, weapons, etc.) but only to an extent.
That’s why Ares is designed to work with skills systems besides FS3 (currently including Fate, Cortex, FFG, and Simple Traits), because my preferences are not everyone’s preferences.
Of course, I can’t stop folks from doing whatever they want with FS3. It’s open source. You can make house rules-- and believe me, I’ve seen a lot of customizations (some good, some weird, some awful) in the 10 years since FS3 first edition came out-- and that’s totally fine.
But FS3 is designed/balanced for a very narrow application (near-future, cooperative, lightly-coded games), and it just doesn’t work very well outside of those bounds. When a game uses it poorly, people don’t think: “Wow, FS3 would be great if these guys weren’t using it in a way it wasn’t designed to be used”, people think “Wow, FS3 sucks.” And when I see those complaints, it makes me sad. So hopefully folks will forgive me when I get grumbly about seeing my “baby” hammered into round holes.
Happy game-building.