Love the upgraded colony defenses...
Love the new cloaking system...
Dislike the Starbase buff for the fact that we don't have a big enough player base to take down a player Starbase at the moment, which basically means our AI Starbases are null and void in the case one decides to make it's way over (Sandtrooper).

Dislike the smart/heat/missiles - Less missiles in tubes with more powerful pop would be neat I think.
Seems slower to turn and Q (which is okay, just different)...
Honestly, I can't really tell a difference in ships from before other than a few modules/tubes missing here and there. I guess I'm meaning speed wise - Seems pretty much the same. (I've only played with Marauder/Destroyer/Scout and they seem pretty equal in speed) I for one would like to see a much quicker Scout.
I haven't put in much playing time though either, so my opinions may change in the future.
Max speed is highly different in the sense of default, previously max speed was based on the boost modules, which was now lowered. boost only gives a minor boost. Scouts are about .20gu? quicker then previously I think.
Starbase AI isn't supposed to be easily take down as they make others useless when you do. It was set to be about 3-4 people, but atm I think it is still to easy, a player starbase aimed with autoaim can take it down pretty quickly. Creates an issue. It's supposd to be superior tough, but if you want it to be easier, read the dev log, therse options on how to make starbase AI damage more normal, or make them immune to damage again... It's customizable. The starbase at 40% damage was easy for me to take down with a couple people, it's still to EASY actually. You just need to play with it more

Dunno what your talking about missiles, they always been in? I never changed those, but yeah, in another post I stated I wanted them to act more like missiles, by slow fire rates and less tubes, but won't be just yet until I debug 1.3.0.
QDrive isn't different, and yes, some initital ships like the dread are harder to turn at startup, however you can upgrade your engines to solve this.