Nice job creating a ship! After reading your RSI post, I see the unique point is the extended shield which currently thinking runs into the "whats possible vs game play" balance. As in, it sounds good but can it be worked into a good game play mechanic without being over powered in itself. Depending the size of the shield, I didnt get a understanding of, but if its a sphere around the ship(s) or just a little larger than the ship would make big difference in this discussion. Honestly if a ship can make a large shield, I would see it as an asset to the fleet but I would say that would be its primary role.
So understanding the ship is a "support ship", lets say its primary function is 1. Shield x area with possibly the ability to rearm/repair/refuel something supportish that wont make it overpowered. The ability to land a ship inside is kinda tilting the balance for me, I love it but I dont think something focusing as a shield should have or much else. As you said it would put much more pressure on the power and shields plus coolers, etc. other parts we might not even account for possibly yet. I would say free up space for more power plants, shields, coolents, etc. and THEN if you have extra space without overloading the ship, add something from support.
The design of the ship you currently have I'd keep but change its focus to maybe a smaller pegasus because I love carriers and it looks like it'd be a great carrier and possibly make another design for a shield support ship which again i find very interesting but cant be a all in one. =]