The problem with Starpulse Wave was that although it was a good ability in the beginning, the ability to stack multiple waves on top of one another was quite OP.
However, in it's current incarnation, Starpulse Wave is just a glorified way of dealing with ordinance and strike craft on a rather long cooldown. The cooldown is something that really shouldn't be reduced, since that would just make ordinance useless against Necrons, but at the same time, the ability in it's current form is meh at best and extremely situational it it's very limited utility
Make Starpulse Wave do substantial damage and ignore armour. This comes with the tradeoff that it also does full friendly fire; making it a very bad idea to unleash anywhere near your own ships.
This allows Starpulse Wave to become a rather impressive ability and well worth the long cooldown, while at the same time removing the tactic (stacking) that previously made this an OP ability. It would then do impressive amounts of damage, but that damage would affect all surrounding ships, including yours.