After playing with this version for a bit, I have to say I like the role change with fighters/bombers/frigates, they now make more logical sense to me, but bombers feel just a little over powerful, at least compared to their previous standing.
I'm not sure whether you were intending to change the power balance like this, but in previous versions even fairly high mark missile frigates died to low mark fighters. Now, this is not the case. With the increased shields and hitpoints of the higher level bombers (more of both than the equivalent level fighters, for all except mk1!), fighters tend to get odds of 30% to hit higher mark bombers at any but the shortest of ranges, which is difficult to obtain while moving. Although they have tons of bonus damage against them, it's often not enough with the 30% odds to actually guarantee they die in any reasonable time.
I think that slightly reducing bomber shields, and taking off a few hitpoints, and more importantly increasing the fighter damage bonus against bombers (perhaps to double the current bonus) would help with this, if you weren't intending to make bombers last a lot longer in combat vs their counter.
Bombers vs missile frigates seem to work fine, and frigates vs fighters also seems to be fine.
One other thing I did notice was that my free-roaming defending fighters would still prefer to target missile frigates, which they now take ages to actually kill - These were newly built fighters, so perhaps the underlying priority table hasn't been updated? If it has, I've no idea why they did that, especially with a bomber being nearby.
I've not found the speed boost to be causing any particular problems, but I certainly don't have time to kite the AI at the moment. It is nice to get a bit of a better response time as I usually play in the slow mode.
Edit: Finally, the damage on a Mk1 bomber seems a bit low - they take a long time to kill Mk1 frigates nowadays. That being said, before this version they killed forcefields and stuff in good time, so perhaps it's just frigates they need to be slightly boosted against.
I hope that helps, and I realize it's all just my opinion of the new balance, but I am assuming you'd rather be told various opinions and decide from there if you're happy with it.
Also, merry Christmas to all who celebrate such!