No doubt, there's a lot of stuff that can be done, but at the same time, it IS missing quite a bit of depth. Seems like the team wanted to do a lot, but pulled it out at the last second. For example, don't know if you noticed, but all the ships are the same speed, this doesn't really make much sense when you have light fighters running around at the same speed as a massive battleship or freighter.
Like BlinderBomber mentioned, the missions could benefit from a bit more creativity, hopefully to be solved in a patch or expansion at the very least.
The universe isn't very dynamic, especially in multiplayer, there are EASY ways to max out your level and ship in a few hours. Mods are being made to fix this, thankfully, so that the multiplayer game doesn't involve everybody flying around in the best ships fully loaded out.
People are even making mods to attempt to bring the game back to more of a Privateer type game (which personally I was hoping for). If you haven't seen it already, visit the Lancer's Reactor:
http://www.lancersreactor.com
Don't want to spoil anything else for you, even with the above comments, the universe is still MANY times larger than older games of the same type.