I will let other guys comment on gameplay, campaigns, etc. My perspective is that of a modder who has worked as a professional 3D model and skin maker.
FE/FE2 are variants of the SF/SF2 system that was first released in the early 'oughts, roughly the same period as CFS3. Both systems had, and still have, strong points and weak points. They both suffered from a lack of development - lots of hard work is required to realize the sims' potential.
To over-simplify a bit, SF/FE got better devlopment initially but hit a plateau when the developer changed his marketing focus to mobile devices. Third Wire has ignored FE/FE2 since 2010, so what development has occurred since then has been due to modder efforts.
Meanwhile, the OFF/WOFF guys slowly developed and improved their mod, initially using the CFS3 system. Over time, they have made so many improvements that WOFF2 now only uses a modest amount of CFS3 code, and only realized the sim's visual potential in the last few years.
What's the bottom line? FE/FE2 is more accessible and easier to mod than CFS3 - that's why there are more aircraft, theater maps, ground objects, campaigns, etc. However, the general level of graphics and immersion for FE/FE2 suffers from lack of development and is now a bit outdated. Simply put, more time and talent has been devoted to WOFF over the years and it shows.