First strike idea i believe. As the attacking ship you should retani an element of suprise even if the defending player destroys you as you destroy him. Tie would have been more along my way of thinking though

Yeah... but here we're talking about the last ship only. It's not going to effectively produce a "first-strike advantage." A system where the first round was fought with pre-1.2 sequential firing, and all rounds after the first were fought with 1.2 simultaneous firing, that would yield something like a first strike advantage. This system looks to me like it's just going to promote weird cheese... Imagine a 7 hitpoint, 24 attack tiny fighter in a 1 on 1 battle with a 6 hitpoints, 24 attack tiny fighter. About half of the time, each ship will destroy the other ship, but in 100% of those cases the 7 hitpoints ship will survive and the 6 hit point ship will die. They chose an implementation that's going to result in some weird reward structures...

What would be a better system?

If both fleets are destroyed, both feets are destroyed. The current system keeps one of the ships alive (based on maximum hitpoints, which seems a little arbitrary?) as if a tie is something that has to be avoided.