I must agree with dfinlay on the essence of the problem he raises, though not on the suggested remedy.
Since one of the goals of AI War 2 is to be more approachable for new players, having modular components on all starships from start for the player to fiddle with or be befuddled by is something that is contraindicated.
On the other hand, having modular components on all starships of all tiers eventually might well be interesting, though leaving itself open for a lot of balancing issues.
So I'd suggest rather stealing a page from other real time tactics or strategy games, of having one default equipment loadout for each component slot on a starship be considered the primary for the role, which is unlocked when you research the tech for the ship. Show it first in the list of loadouts or highlight it or whatever, so people are never in doubt which is the primary/generic choice.
E.g unlock Assault Frigate, you get a stock Assault Frigate with the default loadout and no option to change it, the alternative loadouts greyed out. Unlock Assault Cruiser and you get one with the default loadout for Assault Cruser. Mouseover a loadout you don't have access to yet and a tooltip should tell you what you lack to get access to it.
Thus the player is faced with a choice between five different starships at start rather than 15 flavours. There's time enough to agonize over whether you'd prefer flavour A, B, or C for starship type 1 later on. Don't even think of giving the player that choice from start in the basic game. Make him focus on the starship ROLE to start with rather than min-maxing. So long as the default loadout is one that is good for the role as indicated by the name of the shiptype (e.g. assault, siege) that is sufficient.
Gaining access to the alternative loadouts could then be handled by unlocking them at certain technological milestones, an obvious choice would be to link it to the total tech invested in starship techs.
The latter would tie in very well with an in-game tutorial approach to introducing players to new things.
E.g.
Condition: First research of starship completed.
Tutorial message if enabled: "You've researched your first starship. Starships are large ships designed to fill specific strategic niches with a flexible choice of equipment. For the moment you only have access to the standard equipment loadouts for their primary role, but rest assured that the bureau of ordnance is hard at work preparing alternatives for your use. Spend X total on starship technologies to unlock the first alternative loadouts."
Condition: Spent X total on starship technologies (whether in the same type of starship or spread over several, say X is enough to unlock a total of 4 or 5 mark 1 starship types)
Tutorial message: "You've spent X total tech on starship technologies and the bureau of ordnance construction have made alternative loadouts available for your starships."
or "has made alternative long range loadouts" or "has made available frigate loadouts" or whatever, depending on how many steps would be desired before everything was unlocked.
Basically introduce the loadouts gradually to players depending on their total investment in starships: That makes it easier for new players to deal with by introducing things for them to deal with slower and it provides an alternative resource balancing task for experienced players to take into consideration if they have specific favourite loadouts they want to get access to early.
Even simpler than "X total tech" could be "X loadout unlock points" (find better name) so the player wouldn't deal with adding disparate tech costs to try hitting X as easily as possible but could deal with doing the same with the easier rule of each tier x starship researched providing x points, and then having some nice little counter in the starship construction window showing current unlock points out of unlock points needed for next step.
E.g. If first step is X=10 points, then it can be unlocked by researching a single starship to T4, T3+T3, T3+T2+T1, or T2+T2+T2+T1.
