My guess is that if you have 40,000 ton ships at Ion tech, you are running with reduced research rate or something. It is otherwise hard to have really large ships at ion tech, because if the resources that went into the shipyard went into research labs instead, you would be out of Ion tech in less time than that shipyard could build something.
So if you want settings that really encourage big ships early, something like 10%-20% research rate sounds about right. Bump the economy up by a factor of 2-3, and you get the production capacity to build larger ships and the tech rate isn't going to obsolete them too fast if you are putting similar levels into boosting your research as boosting your fleet production.
I think the biggest advantages large ships have in C# are the shields and the effects of having your best officers concentrated on one ship. If you have an engagement between 8 5,000 ton ships and 1 40,000 ton behemoth, the advantage the behemoth will have in a beam fight is that at extreme range, it can do more damage past enemy shields that they can regenerate. This is balanced by the fact that a multi ship formation could simply withdraw the ship whose shield took damage while the other ships closed.
I would expect that an early behemoth ship would have to get repeated upgrades to its beam weapon fire controls and beams to maintain at least some edge in long ranged beam combat.
Ion tech is a bit early for ECM tech, but capital ships in general benefit more from ECM than smaller ships do.
I have mixed feeling about the troop capacity. My beam warships have cryotroops, on the theory that they will be the ships closest to enemy crippled ships, and already fast and durable enough to close vs a mostly crippled ship, so having boarding capacity on capital ships makes some sense.