Since the premise is that you are picking up resources (as points) at each hill, my thoughts were completely different in how to solve long matches.
As it is right now, the best strat is to cap a point, then hold the enemy there without killing them (Lame Ship Strategy) as one of your ships runs to the next point. If both teams get there at the same time, no points are awarded. This combination is what draws the battles out so long.
My suggestion is that you ALWAYS get points for having ships on the hill. 1 point per second per ship you have on the hill. 1 point per second if you have the hill captured. So, even if no one takes the hill, and you have 3 ships on the point, you are getting three points per second. If you capture the point and have three ships on it, you are getting 4 points per second. However, the enemy can still get points by having ships on the hill.
Example 1:
Red captures the point and has 2 ships holding. That means they get 3 points per second.
Blue attacks that point with all three ships. This means they have 3 ships on the point, so they also get 3 points per second.
Example 2:
Red and Blue fight over an uncaptured point.
Red has 2 ships there, for 2 points per second.
Blue once again has 3 ships on the active hill, for 3 points per second.
In the end, artificial time limits would not be necessary, and matches would go much faster. The 'Lame ship' strategy would no longer be valid. Scores could be nail-biting-white-knuckle-grip without people starting to quit out of boredom. High skill teams could still win without being 'beat by the clock', as in the time limit suggestion. I suppose the game mode might have to be renamed to something like 'Occupy the Hill', or maybe make this Resource Race v2.0.