I personally feel engineers were a mistake it's the same argument I've heard before. Some argue that Solo/PG's are "easy mode" yet those who are making that argument are all engineered to the max and complaining nothing is a challenge with maybe the exception of PVP. And that is why everyone needs to be forced to PVP apparently... because they no longer feel a challenge in the game... It is the same type of argument I hear from the "elite" from all types of MMOs when they get to the high end and gear themselvs to the max they then complain that the game no longer has any challenges and that it somehow is the game designer's fault.
I don't think it's so much that there isn't a challenge, I feel like it isn't very dynamic. The instance mechanics are pretty one dimensional, with very little adaptation required. I think FDEV recognizes this, and built the staged Thargoid responses during combat to address this concern. Also the pirateable megaships in 3.0. It really is just a toe dipped in the ocean though. All of those pre-existing instances we have now: nav beacons, compromised nav beacons, res zones, conflict zones, checkpoints, megaships, distribution centers, debris fields, etc. - there is no special event or boss spawn or threat other than a "critical mission update" which usually is substantially disconnected from the type of activity your currently engaged in.
A high intensity conflict zone with cap ships should be scary for all ships. Not a rinse repeat exercise. It might be fun to have a reputation mechanic that builds the longer you survive in the CZ. More enemies begin to target you as a hated foe. Could apply to a wing too. That would be fun.