There are so many ships capable of fielding strikecraft that the numbers get out of control pretty quickly. Reducing the number of actual polygons out there by downsizing squadrons and increasing damage might help.
Yes, this will be on the list of optimizations.
My second complaint, and this isn't necessarily limited to your mod but includes Sins in general, is that there's a critical mass where trying to micromanage abilities on capital ships becomes futile. Early on, you can micro your capitals' abilities to great effect. But as the game progresses and fleet sizes begin to swell, it becomes less and less practical.
I try to give capital ships intelligent targeting parameters to lessen the amount of micro required. I'll need to spin through the Colonials and see if anything can be tweaked. I've already done this for the vanilla factions and fallen races.
It is indeed a problem though if your trying to micro more than 3-4 things at a time generally speaking. Trying to micro 15 capital ships is outside of my control unfortunately.
It just makes a little more sense in my head for both the capitals and larger cruisers on both sides to be a little larger, meaner, costlier, and less common-seeming.
Colonials have the largest fleet supply per ship in the mod. Cylons will be adjusted up as well. The mod is an expansion mod, so I'm hesitant to change core stats.
Maybe playing with smaller fleet sizes and not building so many capital ships would improve your fun.
I also don't tend to play extremely long games in Sins due to it's normal late game lag regardless if a mod is running or not.