Owning both for several years and shooting them extensively, the SCAR is the better overall rifle.
The FS2000 is interesting and fun to shoot, however it has some areas of concern from my perspective.
First, it's a sealed system. That means the rifle's defense against hostile environments is to be sealed as best as it can be to the elements. This design philosophy is at the root of all the problems I see with the design.
The rifle ejects out the front. This is a novel idea that deals with the problem of shooting the rifle either left or right handed without having to swap out bolts or worrying about where brass is being ejected. However, the shuttle system used to move spent cases up from the chamber and line them up to be pushed down a long ejection chute can be problematic.
Since the rifle lacks a conventional ejection port, if you get a malfunction (and they do happen) you don't have a large hole on the side of the receiver by which you can access the inner workings of the rifle to clear the malfunction. This goes back to the sealed system I spoke of earlier. To give the operator access to the chamber area for clearing the weapon they incorporated a plastic flip-up cover. The cover is rather flimsy in construction I wouldn't expect it to hold up to much abuse. The bigger problem is that the shuttle obstructs easy access to the chamber even with the top cover up. Here's a picture of what I'm talking about.
That's the chamber nestled down in action. The white device you see is the shuttle used to ferry the spent cases up and out of the rifle.
Here's a shoot looking down through the top cover:
As you can imagine, clearing malfunctions can be a bit challenging. I've found that to clear malfunctions you must remove the magazine, flip open the top cover and shake the rifle right-side-up, up-side-down, left and right. Eventually, if things aren't too jammed up, the problem round/case will fall out of the action. If you get a round trying to go in the chamber and a failure to eject through the chute, now you have a bigger problem. You'll need a stick or similar device to poke things, or you'll have to field strip the rifle to get the problem cleared.
The other issue that I've seen people mention in this thread is the fact it doesn't accept anything but GI contract magazines or mags that copy the profile perfectly. You can remove the wipes inside the magazine well and it will then accept other mags, but now you've broken the seal on the system and allow for the ingress of debris. Debris and the FS2000 don't play well together... it causes malfunctions. The malfunctions can be troublesome to clear if they're severe (see above).
The rifles aren't all that accurate. With my rifle I'm lucky to get 2 MOA out of it with optics. It's not horrible, but for a super modern rifle I would expect at least AR15 type accuracy with good ammo. With mine, that's not the case.
I've found the SCAR's I own to be far better suited to regular use. They use a conventional design that is robust and easy to use. The SCAR is also quite accurate despite the thin barrel. Given a choice between the two, I would take the SCAR without hesitation.