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The only mods I've ever seen that are incompatible with CE are beam guns and bounce guns. They introduce weapons with special projectiles that seem to be fundamentally incompatible with how CE handles them. Otherwise, obscure HAR mods, gene mods, every faction mod I've heard of are all in the compatibility list. I think I saw VE Factions - Empire in this list even before it was released to public.
NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a more popular project.