I can certainly see the drawbacks. That said--for me it has been the Foundry content that has kept me coming back. People have been complaining about losing the console clickies, but from the standpoint of someone who does want missions that have a story behind them, it's not going to be any change for me in what I do in-game. I was already mostly using full-length missions for my Officer Reports anyway. Unfortunately the Nagus Dailies (which I used to sharpen my space combat skills) may not make it under the new system, but I am sure I can find a 20-minute fighting mission for those times when I just want to fight, go after an accolade, or whatever.
As far as the fleet I belong to goes...honestly I doubt there will be any changes for us even though we're not that large. We probably won't pursue the embassy (though it remains to be seen what fleet leadership does), but I would say that for my fleet, we have other reasons for playing as a group than the speed of leveling up either ourselves or our starbase.