Scout ships could serve two very important roles aside from direct combat...
First, they could be used to fight structures...timed explosives could be made more useful if it was lower tier (of course it would need to be carefully balanced lest it become OP for early rushing)...for example, it could completely disable all functions of a structure (such as the constructing ability of factories or the use of a lab)...obviously a very long cooldown is necessary (though I think the current one is like 10 minutes)...
Martyrdom could fulfill a similar role, maybe doing more damage or disabling the structure longer, but obviously at the cost of the ship (which is arguably negligible)...obviously it would need to be lower tier as well (I'm thinking tier 2 for both these abilities)...
Vasari scouts already have a unique role of capturing neutrals, though I'd advocate some tweaking to their cloaking ability (changing the AM cost and AI use conditions actually works rather well, I've gotten the ship to use the ability properly and to stay invulnerable for long periods of time)...the cooldown on this could prevent it from being abused for capturing neutrals (plus, it uses AM)...
The 2nd role of scouts would be to deal with mines....of course, scouts already have this role except that mines are generally useless (and therefore so is this role)...I'm sort of hoping that Rebellion fixes mines, making them both more useful and more understandable to the AI...I would go even so far as to say that only scout ships could destroy mines but that is an entirely different discussion...
I do believe that if scouts were better at these 2 roles (and both these roles were seen as actually important), then there would be no need for them to be part of early game combat (at least not in a conventional manner)...
An early game involving 4 units would then require a new ship, the corvette...
I agree that carriers aren't a viable early game unit, but fighters are the only option other than scouts without adding a new ship...
Of course, this is all highly speculative...short term solution, seeker gets HP nerf and illum gets a damage buff (preferably frontal, though I have no suggestion for an exact number)...probably not the most ideal solution but I think it could work, enough to guarantee a competitive early game for the Advent...