Should mention that you should have a review process in place to eliminate old feature flags and old code.

It can also make QA testing more time-consuming, as for any given sequence BOTH paths now need to be tested.

Further, one also runs the risk of introducing bugs into your app, as it's possible to introduce side-effects and unintentional behavior when feature A on was never tested with feature B off. Every flag multiplies the number of permutations.