The new X-plane 10 has a very realistic weather engine, at least graphics wise. The actual modelling of the atmosphere is still off, but so is the case with MSFS.
Terrain wise I think that of Xplane looks much better out of the box, BUT the new iteration uses a new autogen system which has its quircks like powerlines crossing runways, fictional small airports being generated and cities having odd housing and no flats or skyscrapers. Also landmarks are currently missing, but we are promised this will come.
So, while the terrain itself looks much better in X-plane, I think you have a more familiar terrain packed into MSFS.
Airports (see X-plane thread) come devoid of any buildings and objects out of the box in X-plane, whereas in MSFS at least some rudimentary objects are placed.
In X-plane you only have the ramps, taxiways and runways unless you add custom scenery or place objects yourself.
Lighting, however, is VERY realistic in X-plane if you have a good computer!
Flight model depends on what you fly. The flightmodel of PMDGs 737 for MSFS is very good, but also X-planes flight model is decent, although (just like MSFS) the stock aircraft are rubbish in that regard.
Problem is that there aren't too many great X-plane addon aircraft yet. Especially not the bigger airliners. MSFS has a much broader offering there.
Avionics ties in with the above point. X-Plane has support for all kinds of intricate avionics, but its up to the third party developers and modders to use it.
Because of the earlier mentioned lack of many decent addons I find the avionics part in X-plane underused and in its current form therefore lacking.
BUT (again) the analog instruments are of higher quality than MSFS's even in stock aircraft and the framerate or update rate is much much higher than MSFS's. This makes flying hands on a far better experience than anything I have ever experienced in MSFS.
Regarding avionics MSFS has the same problem out of the box, but again, the offering of third party addons is much larger and make for some high quality avionics (PMDG again).
As you can see, there is no package which has it all.
X-plane supposedly has the better fight modelling, but we (modders) need to start doing stuff with that. Nonetheless X-plane does offer a lot for civil aviation enthousiasts.
And you can actually fire weapons off aircraft that have em too... out of the box! ;)
Mid-air refueling, entry from orbit in a space shuttle, carrier takeoff and landings... al there out of the box in Xplane.