What you gain with Pentax :
- Wider array of lenses
- More WR lenses
- FA lenses are full-frame
- Higher resolution (24Mp vs 16Mp)
- Probably a sturdier body (mag-alloy)
- Image stabilization for all lenses (roughly 1 to 2 stops)
- Better RAW support in Lightroom and ACR
- Better for astro-photography
What you gain with Fuji :
- Thinner and lighter body (400g)
- Probably lighter lenses too but not by a huge margin, Limited lenses are not really heavy (but are generally slower)
- Fuji colors
- Bigger EVF
- In-body wifi (you have to buy a Flucard for the K-3)
- Can adapt a wider array of lenses (especially M-mount)
I think AF speed are comparable.
Regarding X-T1 vs X-E2, you lose weather sealing, and get a smaller EVF and slower AF.
If your mostly looking at sharpness, the Fujis will not do better than the K3. Color will be different (a lot of people love Fuji), the Fuji kit will be a bit lighter, the Pentax has IBIS that works for all lenses, and then it is EVF versus Optical viewfinder... what do you like better?
$400 is worth the upgrade to the XT-1, IMO, if you value the EVF (loads better on the XT-1), weather-sealing (with future lenses) and tilt screen.
Viewfinder and focusing are reportedly a decent step up from the XE-2 to the XT-1. I think for the viewfinder alone, the XT-1 is the one I now lust after. XE would be a little smaller, yeah, but I have an X100 for "small."
It you really want to try out the Xt1 (I admit i certainly do), I'd pick up a body only and an adapter and throw your limiteds on it. The EVF with split focus assist would be awfully enjoyable on good manual glass... or at least this is exactly what I'm envisioning trying a ways down the road. If I like the body, I can invest in some new fuji glass later on.
As has been said, the two camera's IQ are comparable, but different. You'll clearly have more crop possibilities with the K3, but depending on how you shoot you may not care.
Check out the write up about the xt1 just posted today at stuff huff blog. I don't have an xt1 but I do have xp1 & xe1. Basically from what I am reading consensus is much faster, ok for slow sport action but not there yet if u need pro dslr speed for professional sport. I ymmv depending on how fast is good enough.
The XT1 is not near as fast as a D4. In good light with the right lenses, the XT1 is almost as fast as an EM1 or other modern m43 body (again, with the right lenses). This is a real accomplishment for Fuji. In low light, though, it slows down and the Em1 really doesn't. On the whole, for S-AF, I'd say that Fuji has finally reached the point of "fast enough". It's not the world beater Fuji claims, but so what. Once you're at a certain speed, it's all just kind of game playing whether one is faster than another. M43 has been at this point of "fast enough" since the GH2 in 2010. It's gotten better but not in a way I'd say matters. Fuji is just getting there and still has some work to do in lower light.
Once place where almost every reviewer (other than Steve Huff) seems to give Fuji a real edge, though, is in tracking AF during burst mode shooting. It's evidently the best mirrorless camera for this, other than the much smaller sensor Nikon V1 / J1. And this is after the EM1 was supposed to have made big strides in this area. I don't use this mode really at all, so I can't provide any independent verification on this, but there seems to be an emerging consensus out there that Fuji got this really really right. I haven't seen anyone compare it as on par to the D4 though...
I can't speak to the K3 - I'd assume a DSLR focus system is still marginally better, at least in lower light and at tracking, but I think this is somewhat lens dependent and I don't know anything abut Pentax lenses except that they sure seem to pack a lot into a small space!