Extra cost with V engines, 2 separate cylinder banks, double the amount of cam shafts, takes more room in the engine bay etc etc.
They can have some very nice traits but with more moving parts it'll always equal more drag hence lower efficiency versus a standard inline 4. One of the reasons the VW VR6 was good was that it wasn't a true V6 as it shared 1 block with the pistons at about 15 degrees rather than a standard V6's 60 or 90 degrees requiring 2 seperate banks of cylinders. Also a V6 is inherently unbalanced, not than an inline 4 is perfectly balanced either..
I'm mostly referring to mainstream car engines not race/specialist engines