Assuming over about 10,000 tons and TL15, looking at best of best and shaving down from there:
Bridge: 2%
Maneuver: Drive 17% + Power plant 6% + fuel 6%
Jump drive + fuel: 12% for J-1 +11% per jump rating over 1, or 12/23/34/45
Meson Screens: fixed 40 dTons + 3.6% (power plant and fuel)
Nuclear Damper: fixed 200 dTons (including power plant and fuel to power it)
Weapons: turrets 1%, bays 5-10%
Spinal: fixed, weapon+power+fuel - call it 2800 for a J, 4000 for an N, 7200 for an R, 9400 for a T. Or as percentages: 1.4%/2%/3.6%/4.7% on a 200Kt, 5.6%/8%/14.4%/18.8% on a 50Kt, and you can calculate for other sizes.
Armor: 16%
crew: ~1%
There's a wee bit of fudge 'cause the power plant and crew don't quite calculate out perfectly that way, but it's a good starting point.
I would suggest that the price you pay in battle for shaving 0.4% or 0.8% off the meson screen just isn't worth it (not unless you're something destroyer-sized who intends to overwhelm the capital ship with sheer numbers, in which case drop the thing entirely and build more ships). I'd say same for damper unless you're flying an uber-armored buffered planetoid. I'd say also that in a meson universe, sacrificing agility is statistical suicide; I can run the numbers if you'd like, but gambling the whole ship so you can throw 5% more at your armor, jump range or spinal mount is never a good idea, IMO. Take the meson out of the picture and we can talk, but while it's pumping out a chance at a one-hit KO, best keep your speed up. So, total for best of all things: 41.6-46.6% + 240 dTons fixed before spinal, jump and armor.
Leaves you about 56% of your ship to share between the spinal, 5-16% armor, and 34-45% jump drive/fuel. Which immediately tells you that either the big gun, the armor, or the jump range are going to have to be compromised. It's also quickly apparent that there's less room for compromise on a cruiser.
On the other hand, the Imperial principal opponent is the Zho. Zho are down a point on the to-hit roll for computer, down a point again on the penetration roll for computer, and then another point (compared to the Impies' odds) for facing a better meson screen than they can build themselves, and then another half point for facing that meson screens with weaker spinals than the Impies can build. (The Zho spinal is bulkier and their power plants bigger for the same power level, but that tends to show up in reduced jump range so affects them more strategically than tactically.) I think it's the same with the Solomani and the Julians: their ships are lower tech. All in all, the Impies have the luxury of a bit of wiggle room because their opponents are generally inferior.
Me, I still wouldn't shave agility or - pity's sake, really?? - the meson screen. Still, the Impies can afford to gamble a bit to make room for other considerations - primarily so they can carry a bigger gun, it seems. Doesn't seem to be worthwhile in space battle - after a certain size, it's just overkill-city. Maybe they're useful in planetary bombardment: a 270 meter kill radius must be quite devastating against ground troops and installations, the more so because very few will have meson screens/computers that can repel it. Everything just flat dies in a circle a third of a mile across. I still think the N-meson is more than plenty, but for some military types it's always about the biggest bomb or the biggest gun.
Cruisers are a quarter the price of a dreadnought, and while the S-9 models aren't worth much against a solid boxer, they are the unholy demons from hell to an undefended world - and there's a whole lotta worlds that lack the pop and tech for adequate defenses. Forget the FFW boardgame and scatter a hundred or so of them into Zho space singly or in pairs with a decent destroyer escort and support, and they tie up at least as many Zho cruisers hunting them down while they go from world to world shooting up the freighters, disrupting commerce, dropping troops down to beat up the local army unit and write, "Kilroy was here," on the walls of the local starport, and in general making the locals very unhappy with their interstellar government for having started a war. 1-on-1, even the poorly designed S-9 cruisers are probably a match for a TL14 cruiser. (Though I'd still - oh, never mind.) Only reason I don't see them wrecking the starports and savaging worlds a la Survival Margin is that it'd be hard to keep the Zho from doing the same thing, by which I infer there's some sort of official or unofficial mutual understanding.
On the subject of forgetting FFW (and maybe a bit of other canon), I would dang well make sure every world with a halfway decent population had at least one meson-spinal-based planetary defense battery at my best tech for just that reason: only way to keep my worlds from being savaged from orbit by nukes and mesons is to give a credible threat to the attacker. A deep meson site is cheaper than a ship and persuades the enemy to either keep his distance or come in greater force to take out the threat. I find mutual understandings are ever so much more effective when backed by firepower.
Very ritualized, these interstellar cultures. Fight more like the Aztecs than the Romans.
