Have a short cooldown on actually building the dread (like 10-60 sec) but let the antimatter go up really slowly so the antimatter in effect controls how long it takes.
do the antimatter get lost even if it is not built perhaps?
You might as well just have a short cooldown ... so the problem is that the player would get several dreadnoughts (cooldown triggering is very basic for abilities) and nothing else (or a small number of other ships) as the fleet logistic slots are filled.
This still does not address your major concern regarding Dreads ... " with the dread factory, i can just turtle and build up more and higher level dreads and then steam roll the map... i dont uppgrade either my fleet cap or my cap ship cap and i can still roam around with 20 dreadnaughts. pretty overpowered.. " firstly that's a 10 hour+ game you are playing (Dreads are produced every 30mins), I'm surprised the AI's didn't come visiting with its Dreads and capitals.
Now based on your comment ... "Hmm, i dont know abouth slower build, the ai generally just uses them as stronger capitols, they really only shine when you get them to lvl 6+ and can transform them. So unless you could let the Ai get them at lvl 10 i think the current build rate need to stay because they die real fast at lvl 1-4." Maybe the thing to do is back-off the Super-Dreadnought enhancements.
By the way did you notice the problem you described before, that is with the pirates, playing diplomacy 1.21?