The first few hundred cycles are definitely slowest for me, I think that's down to constantly pausing and planning while trying to make the base stable and livable. I only keep an eye on the timer for the first hundred or so cycles anyway to see if I can get the carnivor achievement that run.
When everything just works by itself you won't need to pause as much to keep an eye on everything, the more you automate any one system the less worried you'll be about that system breaking.
I also have a low dupe count on any planetoids I colonise. When there's only 2 dupes on a planet it takes an eternity for anything to get done even at 3x speed, not much need to pause.