I own both FSL and Epilog lasers so I'll put in my 2 cents...
(tl;dr version: They are different animals, so a comparison between any Epilog* and any FSL Hobby series machine is likely to be unfair.)
FSL
I bought a FSL 45W 5th Gen laser about 3 years ago. And another 2 years ago...
They are not bad for the money. They are good, but they are not an Epilog. The rasters are fine, and the vectors are good. I found that if you had really fine raster lines next to each other, it was often difficult to get consistent results. Between the stepper motors, the belts, and the bearings, they could get sloppy over time. Also, the glass tube laser can't really turn off and on fast enough in some cases. Cooling was occasionally an issue depending on the season. The fact that the bed couldn't be independently leveled was another thorn in my side.
The focusing on the FSL is... well... not quite a joke, but honestly, they could have done better. The roller adjustment on the x-axis rail - that gave me convulsive fits. Too tight and the head binds and won't move. Too loose and your rasters look bad. Finding the sweet spot feels like an accomplishment! Until the wheels wear down and you have to readjust.
But, these are pretty lightweight machines. The belts stretch. The bearings go bad. A lot. I was replacing tubes about every 6 months on each machine and power supplies about every year. Bearings lasted me about 3-6 months. The coating on my lenses would often flake off.
Also, the software/driver was rather slow. On some very complicated projects, the file could take 15 minutes or longer to render before the machine could be run. The software on the computer actually controls the laser head over the Ethernet cable while the job is running. That means that if the computer crashes, or if the ethernet cable gets jiggled loose, the job fails. (note: There is a way to load jobs on a microSD card on the FSL, but I never tried it - so that could solve this issue.)
Epilog
I bought my Epilog (40W Mini) last year.
It was expensive. I could have bought 4 of the FSL's for the price. The rasters are great and vectors are awesome. There really isn't a comparison in output quality of the tubes. The RF tube on the Epilog is so much better than the glass tube on the FSL. But, they also cost about 4 times what a glass tube costs. And here is where I am nervous about my Epilog. My original tube died at almost exactly 6 months. The replacement tube lasted 45 days. Both were covered under the warranty, so I'm not out any money yet. But, I sometimes worry that I'm running the laser with a $2000 gun pointed at my head.
However, the difference between the servo motors on the Epilog and the FSL mean that the Epilog is twice as fast as the FSL on rasters. On vectors, they are pretty comparable, but the Epilog will edge out the FSL.
The motorized z-axis and the fact that the bed can be independently leveled means that I can get more consistent results across the surface.
As for the software, it's nice and fast. I've yet to find a file that takes more than a 30 seconds to send to the machine. And that brings up another difference: the FSL is run "live" from the computer while the Epilog is run from the laser's memory. Specifically, the FSL can only hold 1 job in the software, while the Epilog can have dozens held in the laser's memory.
Summary -
My problem was that I started off as a hobby - which turned into a business. The FSL Hobby machines are not designed for the volume that I was running. So in the end, I had to step up to a better machine. And that is why I think that any comparison against any Epilog from the Mini/Helix series or higher is unfair. There is almost no overlap in the parts used between the FSL or the Epilogs. The tubes are different technologies. The bearings are different. The belts are different. The machine/bed structure is different. And... the prices are completely different.
A much fairer comparison in my opinion would be the FSL Hobby vs the Epilog Zing series. I think the FSL Pro series would stand up better to the Epilog Mini/Helix line. But, the FSL still struggles due to the glass tube technology.
P.S.
If I was buying another hobby machine (or if someone was looking for a hobby machine) the FSL 5th Gen Laser is still a good starting point. It will perform at 80-90% of an Epilog but at a much lower price point with tech support in the US. My only caveat is the Glowforge machine - I haven't used one yet, but they look like a really strong contender - *if* they pull off what they claim. And, that "if" seems to be pretty strong. They missed their December'15 shipping dates and are now projecting "first half of 2016" for the first machines to ship.
*The Epilog Zing series would probably be a better comparison to the FSL Hobby. Both use stepper motors and roller bearings. However, the Epilog still uses the superior RF tube.