Okay a few things...
First die roll defenses - I said these were not purely balanced 50/50 as the defender gets to wait and see if you succeed in your first roll, if you fail and you spend he gets to see if you succeed in you second roll. Only if you succeed in one of the above does he have to spend. So if the roll is 50/50, and you take two shots at it you should still fail some portion of the time, in which case the defender will not spend. It is true if the attacker succeeds and the defender then fails to force a failure on the reroll it will balance out, but this has been less common in our games.
The above argument has become wasted however as Matt has ruled you can't re-roll a re-roll so only one player can actually cause the die to be re-rolled. IE if the attacker succeeds the defender can try to re-roll, if the attacker fails he can try to re-roll but the second roll stands.
As too the crit chart, yeah, being able to roll twice for the second die is huge, first die is nice but two shots for an x-6 roll is a big deal, and a much bigger deal for multiplier weapons.
The refit and other duties tables are not equal, I agree with that. My question is more are they so unequal that we are better off playing without them. The same can be said about the special rules for races. The abbai rule about a turn of peace getting them extra cash is by no means even vaguely equal to MoD. Is there a balancing element between the charts and the fleet strengths. (excepting the one really bad Narn roll...I think that was honestly thought to be a bonus, and just not thought through.) I think that would have to be looked at on a case by case basis to see where folks thought things were weak.
I don't think there is any real argument to be made about CQ improvement or ship damage repairs after the battle. All races should be able to benefit from these if they chose or not without being at a penalty or bonus.
Using exp dice for special actions/damage control is somewhat different. Certain races are more dependant on these types rolls than others, what I am not sure of is whether those races get an unfair advantage out of it. The ISA and damage control certainly concern me as they are one of those bleeding edge races...balanced so finely that one wafer thin mint is all it might take to make a real mess of things. Vorlons...not so much. Drazi...well...lets just say I still think in campaign they need help, and the nice lady with the couch is not what I'm talking about.
Anyway..tried to keep this somewhat general as we'll hash out the direct stuff for our campaign based on who wants to run what and what house rules/fleet style we use.
Ripple