CFS3's strengths were in different areas. It was easily moddable, but had inferior graphics abilities (the water isn't transparent but a solid "water" texture for instance). The map of Europe was far larger than any Il-2 map, covering from the UK to Switzerland and France to Germany. The AI was more believable to me, it never pulled stunts I thought impossible. The damage and flight models of the stock planes were poor (almost any hit seemed to go for your control cables first, making you roll like a B-52), but 3rd party planes from modders and paid sources like Firepower were excellent.
I found the dynamic campaign better done than the ones Il-2 generated, too.
Frankly, I think overall CFS3 offered an equivalent experience, less in some areas, more in others, to Il-2, but the community at large seemed to embrace Il-2 and shun CFS3 and it faded away. The leaked screenshots of the unannounced-yet-cancelled CFS4 in the Pacific theater were quite impressive and honestly looked better than Il-2. We could've had a great new WWII sim circa 2006 from MS had they not cut and run. Alas...