Some good stuff to come, though I hope they don't go too overboard with new "systems" (like Reputation/Romulan Marks, Omega Marks, etc.) in future - too many currencies already, and most of these things are just resource sinks; the old saying keep it simple applies even to Trek.
Nevertheless, some real strides are being made, and it is clear that the Devs have listened to some of the suggestions from players (some...).
I will remark that just the simple addition of an option to switch characters as opposed to logging out, then back in with a new one is THE best new feature so far; worth it by itself!
(...actually active since November 2010, which may one day be important to archaeologists, but not to anyone else...)
The dilithium costs for Duty Officer actions at Star Fleet Academy are a huge mistake and will impact small fleets and solo players. These changes will drive casual players away.
The reputation tab will further dilute material you might donate to fleet projects and adds two new marks you'll have to grind in order to collect (and more dilithium costs, albeit relatively small to start out).
The daily patrol in new space sector was fun but time consuming (one system mission finished around 15% of objective and most usually take 5-10 minutes). Nothing really new or groundbreaking, just more scanning, beaming, fixing, fighting. Or more appropriately grinding.