actually the last levels are pretty easy
max out you guns, and resource gain and max recycling.
just pass some time and only deploy to counter, while getting your guns(artillery and torpedo),
then when you hear the music change and a whole lot of enemies incoming, spam destroyers and frigates and 2-3 battle ships, add destroyers and battle ships as you see fit.
also the fortress is evil with artillery >_>
because you can hit the enemies base with artillery then :S
okay 1st thing i see here is something that isn't really that handy to work with becuase it depends on the frame rate, wouldn't it be better to use an interval, in a lot of cases a named interval(meaning that the interval is named to a specific spot)? you use it like this(this way you can also name intervals with a for loop, or something along the lines of repetition), but i'll just use a for loop to make it easier to understand=>
for(var i:Number = 0; i with the amount of time you want the interval to re-execute the function in,
you can clear an interval with
clearInterval(address of the interval)