We have been playing Mag Blast (primarily 2nd edition as 3rd is a bit flawed) ever since it came out. Probably more than a thousand games. Obviously even the short rules, albeit almost perfect, have some questionable or debatable areas. I haven't seen a lot of Mag Blast errata around so below is what we use. I've also included our favorite play variant, using 2 flagships.
Fighter/Bomber attacked by an enemy fighter may not be attacked by an own fighter (but temporal flux is allowed).
Yssaril: Blast or squadron on a fleet (not a flagship). (changed because this is how it is in 3rd edition)
Naalu: Can't be evaded (it's a power, not a shot).
Jolnar: Not a flagship.
Boarding: Aquired ships may already launch squadrons during your own player turn.
Emp cannon not effective against flagships.
Missed taking Lizix two free cards:
If not cards discarded yet (=next own turn) - pick two now.
If discarded already, next time Lizix happens, take 3, choose 2.
Start with 5 ships in zones around the flagships (placed randomly, 5th usually in N or S zone).
Special rule for two flagship games: No flagship is active during the entire first game turn.
Special rule for two flagship games: Only use one flagship playable power per player turn (i.e. Xxcha could be used both on an Off and Def turn). Automatic powers like carriers, 6 cards etc do not count.
Mentak, Xxcha, Yssa, Sol, Naalu, Jolnar = Playable
Hacan, Sardak, Lizix, Letnev = AUTO
As for using two flagships I'll give a few comments here. Works well for 2 player games. With 3-4 players not having the flagships active during the entire first round can be too deadly for the players playing last. This is the game mode we play most (if we have time). It makes the game take a bit longer, especially if you start with 5 ships in the zones. With 2 flagships in the center, zones work as they do usuallly basically giving N an S zones a choice of which flagship to shoot at. It also gives you a possibility to use one of the flagships as a barrier in a zone (like having a strong dreadnought) which is quite useful when using the playable power addition.
We don't keep flagships active during the 1st turn as it's often deadly to get hit with with two flagship powers in the beginning (especially if it's xxcha which then robs 3 cards during the opponents 1st turn.... byebye). And yes, that means Hacan only gets 5 cards the first turn .
We don't allowe both flagships to function at the same time *if* you can select the action. Getting hit with two flagship powers especially if one is Xxcha simply seems too powerful. Similarly two defensive powers can stop almost any attack.
If someone tests this and enjoys it, please comment here.