Fuji has better IQ than m43 (admittedly, I haven't used the latest 20MP m43 sensor, but the E-M1 is still on the 16mp, which I am quite familiar with). Of course only the X-Pro 2 actually has extra resolution - with the exception of that body, all Fuji bodies and most modern m43 bodies are 16 MP. The X-T1 (16 MP Fuji I have the most experience with - I presently shoot the Pro 2 with a T1 backup body) has quite a bit (more than a stop, maybe 2) of extra dynamic range against 16 MP m43, plus there is extra apparent resolution, which is probably a combination of XTrans and lower noise, even at modest ISO. Once you jump to the X-Pro 2, there is no real contest. Also remember that Fuji gives you 1 additional stop of DOF flexibility for any given maximum aperture (and the m43 lenses are generally not faster to make up for it).
Both offer fairly complete lineups of excellent lenses. m43 has an advantage in that they also have a significant number of cheap lenses - all the Fujinons are quite good, but you'll pay for them... If you want to add a cheaper lens in a focal length you don't use often, there is likely to be an m43 option, while the only possibility for Fuji is a manual focus Samyang/Bower/Rokinon.
The biggest advantage to m43 (other than video, where m43 has a huge lead - the X-Pro 2 is the only Fuji that shoots decent video at all, and it's quite good, but not 4K) is the Olympus "Hand of God" image stabilization - it really is amazing, and it'll stabilize anything from a lensbaby to a $1500 pro lens. The long Fuji telephotos are just as good(I've gotten shots at stupid shutter speeds with the 100-400, sometimes pushing it with the 1.4x on there as well), but the primes aren't stabilized, and the stabilization on the shorter zooms is decent, but nothing like the long stuff.