They encourage proprietary software and locked down systems. For instance, they use Google play services instead of microG and they promote the play store. I personally think that F-droid apps are much better from both an software freedom perspective and a privacy perspective. I'm not against people installing proprietary apps as I realize sometimes that is unavoidable but they could at least encourage the use of Foss. Graphene could simply have both F-droid and Aurora store by default and on setup explain the difference. They could even allow the install of Play services instead. However, they don't even really try. They focus on security which at the end of the day is subjective.