One problem I've been noticing is that the way the battles are decided seems to be really in favour of the larger force, inasmuch as... Say I send sixty ships over to a planet with fifty on. More often than not I'll be left with about fifty. That seems to be something of a balance issue, because that means that whoever controls most of the map is basically guaranteed to win.
I don't know how it figures who wins what, I know most cell games just do X-Y for X attackers and Y defenders and that seems a bit basic, especially for the AI on display here (which is amazing, by the way). Maybe random numbers are the way to go, that way an advantage of one ship won't guarantee victory and huge forces will still very generally speaking completely trash the enemy force.
The virus is airborne. Nothing can save Madagasc- oh, shit, they shut down their docks. Our evil plan is doomed! Even though airborne viruses don't need docks!
Here's a bit of advice: When you get the 10% health boost upgrade, use it as early on as possible (but after you've dropped the bonus penguin). It adds X% of what's left to your penguins' health, so the more there is left the better the boost. They aren't going to lose health at any different rate, either, so you'll have maximum time.
 "Solarmax 2"){kind=icon}
 "Pandemic 2"){kind=icon}
 "Bloons TD 5"){kind=icon}
 "Flight"){kind=icon}
 "Pirates of the Stupid Seas!"){kind=icon}
 "Proke"){kind=icon}
 "My \"Dear\" Boss"){kind=icon}
 "Treadmillasaurus Rex"){kind=icon}
 "Accelerator"){kind=icon}
 "Papa's Freezeria"){kind=icon}
 "Portal: The Flash Version"){kind=icon}
 "Synapsis 2"){kind=icon}
 "Bloons Tower Defense 4"){kind=icon}
 "Line Game"){kind=icon}
 "Penguin Overlords"){kind=icon}
 "Whack Your Boss!"){kind=icon}
 "Bubbles 2"){kind=icon}
Surely you mean *faster* than the speed of light ;)