Okay, I get the issue. There are two main things that have influenced what I've done so far, first one is mentioned in an older update note.
"There is a huge amount of flexibility in this system, but if you're modding just do bear in mind that not everything possible makes the most sense.
For instance, stacking too many bonuses on ships is probably not a good idea. One, at most, ought to do plenty fine! Not everything even needs one! It's a matter of whether or not we can increase the interest of a ship's role with this, not whether we can make yet more stuff to read and more mental gymnastics for the player using them."
Extra bonuses are fairly simple to add on. Doing that is in a bit of a violation of the above, however. Admittedly, that's not set in stone! But it's something I'd be a bit reluctant to start doing officially, unless Chris thinks it's the way to go. There are a few units that actually do have several bonuses (Pike units are a good common example), so you could say there's...not much of a problem there? Still, it's a fairly simple secondary bonus.
I think there's an intention for things to be much clearer and simpler to understand here than in the first game, hence the reluctance to add more things in to read.
The second is...things like V-Wings are the way they are, because I've kept to their original incarnation. I don't know the reasoning behind it, but I've always tried to make it work. Giving them a damage bonus is then running into the first thing. They could technically change, but it is slightly bothering personally, kind of overriding what someone else did. I don't know what the attitude towards that is, since this is the first time I've been involved in such a thing like this.
The old hull system might be pretty simple, but I don't know why that was decided against. The current stats would...I think still be pretty usable? For the whole "immunities everywhere!" problem. Things like personal shields, and bypassing those etc is fairly neat so they'd probably stay?
Essentially I've...just tried to stick to what seemed to be rules, or a general desired idea, complete with all the difficulties associated. I'm just a volunteer - I don't want to go ripping up what Chris desired, for it is his game and all. Tried to work with what was there.
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Despite that, can somewhat entertain a few ideas here. First, from my little Classic experiment the economy can be transferred over from what it is now, to nearly exactly what Classic had. A few adjustments from there, to compensate for unit caps being fairly different (which I did) and it seemed much better.
Second, setting the unit caps to increase by 0.5 per mark instead of 0.8 (of the original value, so cap of 60 = increases by 30 each Mark), then removing the damage bonuses increasing with Mark, then changing Starships to be Cap 2 instead of 1 (complete with different values) causes the scaling to match Classics exactly, e.g
Classic, 96 Mark 1 ships of 1x power, unlock Mark 2, 96 Mark 2 ships of 2x power (resulting in 3x total combined).
AIW2 copying it, 60 Mark 1 ships of 1x power, unlock Mark 2, 90 Mark 2 ships of 2x power (also resulting in 3x total combined).
(Apologies if I messed up that explanation, was hard to think of any way to do it).
That also fixes Starships scaling even better than Fleetships (because you can't increase a cap of 1 by 0.8, so it rounds up, the next one rounds up, and so on).
Third, units could get multiple bonuses. First have to note they're multiplicative, i.e if a 2x and a 4x bonus trigger, it ends up as a 8x result. This allows the interesting possibility of...a unit being able to be a small counter to target A with a 50% bonus, a better one to target B with a 100% bonus, but it gets both vs target C, resulting in a 300% bonus (damage increased by 100%, then that combined is increased by 50%). But as noted way above, this could get confusing and clutter things up, possibly. I didn't have trouble with it in Classic, so not sure how it is to others.
Lastly, the planet gravity well could be increased - this was mentioned previously. In testing this does allow you to be able to bypass a lot of the defenses of some AI planets, helping to reduce the annoying grind and compensating for the current lack of transports (far as I know, they will return). This is a fairly risky change, as it's not exactly possible to go BACK if it doesn't work out.
Just ideas to toy with. Not at all confident right now in being able to pull it off, though.