1. Git gud

2.When you pause the game via Esc or the skill menu it does not count on the timer!
That means to reskill as the situation requires it.

3. Obviously dashing is faster than regular running. The problem is you will use your dashes up quickly and will have to resort to regular running again, to solve this use right mouse button to get into semi slow mode where you put down your markers to dash to them but only put down one marker each slowdown. the advantage of this is you have infinite dashes and you dash further.
Problem is for a short timespan you are in slowdown, but this timespan will be miniscule if you time it right

4. You might want to turn ruiner finishes off in the gameplay menu. It will save a lot of time because Mr. Ruiner is in slowdown time doing his cool stunts the timer continues, each finisher will cost you about 1,5-2 seconds, they don't sound much at first but they will add up.
The only real advantage is they can get you out of a tight spot because they give you +1 health and +1 energy.

5. After reaching level 11 you can reskill to overload in long halways for infinite dash which can save you a lot of time.

6. After reaching level 9 you can stunlock bosses with the ramstun. This will make most bosses very easy.