Hmm.. well, I have always found boarding quick and easy once I got my head round it. Not too tricky to teach either. I would be hesitant to change the mechanic too much since it is such a key weakness of big ships in smaller points games. Most changes I can think of that would simplify it make the defender a fair bit tougher.
SAW rules could use a looking at, there are so many many rules and mars that complicate them. I know after a while it gets easier to remember which out of acrobatic pilots, vertical dive or big fuel tanks applies, but I bet it could be simplified.
Targeted shot rules need a review since they are simply never used.and could add to tactical options. Could be a useful mechanic with simple alterations (e.g. choose a targer system out of generators, engines or weapons and take a -1 to hit penalty. If you beat the dr apply the effect and 1hp of damage)
Most generators are easily fixed by activating at a more appropriate point in the activation.
Designing a model sounds very... intriguing!