My biggest qualm with the game is how much the player must rely on luck to get big chains. Sure you can wait for the perfect moment to start a good chain, but after that you can do nothing except hope the game spawns enough ships to make the chain last a long while.
So, some additions to consider if you make a sequel:
-Add a timeline or minimap to show the player when big ships are about to spawn.
-Giving the player some control over booster pickups. Let us choose which ones to pick up, use, and/or remove at will. This will also have the benefit of giving us something to do while a chain is going on.
-Diversify the game's progression with non-linear upgrades.