After accepting the mission to recover the artifact from xenophobes, the game begins to stutter frequently but irregularly. This doesn't seem to depend on graphics settings or what's on screen. It's noticeable even without time acceleration on, suggesting certain ticks are taking a very long time to calculate. I haven't observed this in previous versions. It might be worth looking into whether some of the new AI code scales badly with number of ships.
Pre-1.9, the algorithm for firing was:
For each independent weapon:
Look for the best target for this weapon
Check to see if there are friendlies in the way. If not, fire.
In 1.9 I changed this to:
For each independent weapon:
For each possible target from nearest to farthest
Check to see if there are friendlies in the way. If not, fire and go to next weapon.
Pre-1.9, if the best target has friendlies in the line-of-fire, then we didn't fire at all. In 1.9, we keep checking for other targets that might be accessible.
But the problem with the 1.9 change is that we potentially check for friendlies many times per weapon (once for each target we check). If there are many ships in the area, the performance of the line-of-fire algorithm dominates.
In 1.9 Beta 4, I've reverted back to the pre-1.9 algorithm.