I voted for the Alert improvements. I proposed in the related thread that there be an alert post which causes and alert when enemies are present on the planet. This way you can chose what you do and do not wish to be alerted about.
As mentioned, some of these special structures have so little health that alerting after they have been attacked wont do much good.
I'd give a 2nd vote to the transport improvements. Being able to release individual types of ships, or even individual ships, is something that I'm surprised hasn't already been done.
I tend to vote for options that polish the existing features over completely new features.