I like where you're going with the whole module thing though it does have potential to unbalance the game, at least temporarily until it's re-balanced. I think the best idea would be to have several modular ships but that each of them have only a few choices of modules, so that you could choose what situation they'd be good at. I don't know if you want to add modules to starships that already exist but that would probably require lots of rebalancing. What I would suggest is the following, should you be willing to listen. Remember though I am just a regular gamer and am only giving my opinion and am just trying to help.
Have several modular ships but limit the modules for each one so you can choose between several specialities for each depending on the situation. Each 'slot' on a modular starship holds one item/equipment but there can be several different types of modules on a starship.
Example:
Riot Starship: Specializes in taking out numerous smaller ships I believe.
Slot 1,Weapon: Shotgun/Lightning or some types of short/medium range for taking out smaller ships
Slot 2,Engine: None(regular), Shield Recharging(ship moves slow but can take more damage), Fast(ship moves faster but takes more damage)
Slot 3,Special: Shielding, some other type of item that could be equally benefiting as shields.
This is only an idea but I thought I'd just throw my thoughts out. I thought maybe if there were several modular ships you could choose between limited specialities for each. So for the above riot ship you could choose a shotgun, plus shield recharging engines, plus maybe heavier shields to specialize in taking out a lot of smaller ships. I just threw lightning in there but I'm sure there's something else that would be more realistic for an alternative. Also the reason I put the modules for the Riot Starship as close range is because I thought it might be cool to have other modular ships where one might have several longer range weapons but less shielding options and another might be better for taking out bombers.
Also something seems funny about the whole shield over the ship. For one the shield looks to large within the fleet. Also how none of the stronger ships such as flagships don't have them seems weird. I do have another suggestion about this that may be viable. If instead of having a full forcefield animation you could also make it so when you add a forcefield it adds maybe some kind of glow or smaller graphical circle effect around the ship. Another thing you could if possible is make the current forcefield you're doing for the modular ships smaller so it just fits around the ship, but also if it were possible to make it shrink much slower. So it still has the same hp but looks smaller and shrinks slower.
Anyways sorry if I'm bothering, offending, or just annoying anyone entirely. I've always had a passion for RTS's as well and to me this game completely revolutionizes them. I just want to help in any way I can so if you think either that these ideas won't work in the current game or are just plain crap, don't hesitate to tell me, I won't take it the wrong way.
EDIT: I also realized when I built turrets on the riot starship they seems half in the ship and half above it, a little messed up and not pleasing to the eye whatsoever. I apologize because I know this is prerelease and still of course nowhere near finished. I was just going to suggest maybe if there was a way to make the turrets always on top. On top as in like when a starship flies over another and you see it completely on top. But then as long as you can make it so you won't see the turrets on top of everything, ie if a regular starship flew over the riot ship and you could still see the turrets over both.
EDIT: Also I have a side question while I'm here, I hope I'm not disobeying any rules or anything just thought I'd ask while I've posted here. One thing I don't understand about the AI in general is how certain planets can be alerted and some can't. I would understand if they were humans but aren't their cores, the main centers you have to destroy, kind of like their main brains, like skynet from terminator. If that were true once you attack one AI planet wouldn't all of their planets know you were there? I don't quite understand this.
EDIT: Sorry one more thing, I promise. Is there any way to set formations for your ships? I saw a control node that had some sort of formation setting but couldn't figure out exactly what it did. Like is there a way to make fighters always in front, then bombers, frigates, starships, and long range ships?