One of the tedious things about late game Galactic Civ 2 is when you would face a large series of very weak fleets that you just had to slog through to get to the end goal.
Endless Space has the same problem, and actually it can get to the point where its almost a bug (the AI can throw endless streams of cheap ships that prevent your ships from moving).
I have a suggestion to eliminate both issues.
Suggestion: If your fleet is engaging a fleet that is woefully inferior to it, then two key things happen:
1) The battle has no inputs and no animation, the battle is done instantly (this could be made a preference option for those who really want to see every battle).
2) The battle costs no extra movement to your fleet. Basically its a runby attack, you killed the enemy so easily you didn't even have to slow down.
I think this helps ride the line between an attrition war, where you are facing fleets of cheap, but still effective ships....and a mopup effort where you are just going through the motions of finishing a race off.