Just to articulate a few more points on each side:
To Andreas point, one issue with contravariant in base is that there are no types in base that would serve as reasonable instances. You'd get a scattershot pile of mostly 'nonsensical' instances for stuff like the GHC.Generics types.
On the other hand, but a far lesser concern, it'd shed the dependencies the package has, which would be good for things like lens-style Getters which use the constraint. Being able to use or supply more types of lenses with no dependencies is a minor good point.
On the other other hand, rehoming a lot of the 'nonsensical' style instances to the packages that have their dependencies inverted is a fair chunk of work.
On the other other other hand, this would fix the weird dependency inversion between StateVar and contravariant forced by the haskell platform.
Er... that is a lot of hands. I personally don't care much one way or the other. Doing nothing is literally the default option. If there winds a lot of noise against this I'm happy to stick with the status quo, which is not THAT broken. On the other other other other hand, if there is a huge upwell of support, we could make a go of it.
-Edward
Note to self: I need to stop counting hands in unary.