protip: install a full linux distro on your chromebook, and then use non-google end-to-end encrypted services such as firefox sync or owncloud for dealing with private data.
GAFE is really convenient in a lot of ways; the EFF is absolutely right to complain though that there are a lot of privacy issues baked into the whole thing by virtue of it being Google Services.
Outside of data collection, the issue is that GAFE admins are still at the mercy of Google changes. We may get advanced notices from Google about changes and certainly some are optional, but things like G+ integration, Photos, and so on are completely outside of our control.
My last workplace used GAFE for the University, and we had a lot of very basic privacy things that popped up as a result of GAFE and new gmail features pushed out. Our few privacy minded users (mostly older professors) would get really upset over how much data got sync'd between LDAP and G+ without our admin realizing it, students who had legitimate privacy concerns (harassment cases) were frustrated with the same issue, and so on.
I'd like to believe Google could just ease up the data collection from schools and businesses - it can't be that great compared to the public at large, and it would make GAFE absolutely perfect for schools. (Seriously, privacy aside, GAFE is otherwise perfect for a University set up. Unlimited space, great for student collaboration, and honestly many universities could do away with Office subscriptions at this point since the Google Office Suite is close enough for all intents and purposes.)