I like to propose the following way to warn about instances that are unwanted by some programmers. First step is to mark the instances at their definition site like so:

{-# WARN_INSTANCE tuple #-}
instance Foldable ((,) a) where ...

{-# WARN_INSTANCE tuple #-}
instance Functor ((,) a) where ...

{-# WARN_INSTANCE tuple #-}
instance Foldable ((,,) a b) where ...

{-# WARN_INSTANCE tuple #-}
instance Functor ((,,) a b) where ...


This way, all the above instances are collected in an instance group labelled 'tuple'. At the use sites we introduce a GHC warning option like -fwarn-instance=tuple. This warns about any place where any of the 'tuple' instances is used. We can either place

   GHC-Options: -fwarn-instance=tuple

in a Cabal package description in order to issue warnings in a whole package or we can put

   {-# OPTIONS_GHC -fwarn-instance=tuple #-}

at the top of a module in order to enable the warning per module.

Another candidate for an instance group might be 'numeric' for numeric instances of functions and tuples in the NumInstances package.

What does it mean to use an instance? I would say, if omitting an instance X Y would lead to a "missing instance" type error at place Z in a module, then instance X Y is used at place Z.

There might be an even more restrictive option like:
   -fforbid-instance=tuple

This would not only warn about an instance usage, but it would cause a type error. Essentially it should treat all 'tuple' instances as if they were not defined. (Other instances might depend on 'tuple' instances and if the 'tuple' instances weren't there the compiler would not even reach the current module. I do not know, whether this case needs special treatment. We might require that any instance depending on 'tuple' must be added to the 'tuple' group as well or it might be added automatically.) The advantage of a type error is that we see all problems from 'tuple' instances also in the presence of other type errors. Warnings would only show up after a module is otherwise type correct.

This solution requires cooperation of the instance implementor. Would that work in practice? Otherwise we must think about ways to declare instance groups independently from the instance declaration and we get the problem of bringing the instance group names into the scope of the importing module.

A separate discussion must be held on whether -fwarn-instance=tuple should be part of -Wall. I think that people should be warned about 'tuple' instances early because they won't expect that there is a trap when using 'length' and 'maximum' and so on.

One might also think about generalizations, e.g. whether

   {-# WARN_INSTANCE tuple, functor #-}

should be allowed in order to put an instance in several groups or whether there should be a way to compose a group from subgroups.

Another topic would be a form of instance group disambiguation. Instance groups might be qualified with module or package names. I think package names are more appropriate, like so:
   -fwarn-instance=base:tuple
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