I would suggest to keep a uniform tonnage for your main combatants. Basically, your 6,000t Ark-Royal could take 2 more 6,000t ships with it through a jump gate. If you take one Agincourt and one Illustrious, then you are effectively missing out on 3,000t of extra tonnage that you could take along. Or put differently, you will need a larger number of Ark Royals to get the same tonnage through with a squadron jump. Since the Ark Royal is by far the most expensive of your designs, this is a considerable inefficiency.
Also, the Ark Royals are currently the most crucial ships in your fleet. If you lose these, you simultaneously lose all combat capacity (no active sensors) and all means of retreat through a jump-point (no jump engines). This is not necessarily a big problem, but it certainly does warrant extra protection for these ships. I would therefore advice to upgrade the armour of the Ark Royal specifically. You could do that at the expense of some fuel storage unless you have reason to pack as many.
In addition to what other said about your missiles: The warhead of the ASM should be increased considerably. If you look at the proportions you can see that your AMM has a strength 1 warhead one a size 1 missile, while the ASM has a strength 2 warhead on a size 4 missile. I would heavily suggest that ASMs should pack more punch/ton than AMMs. At the very least get the ASMs’ warhead up to 4, so you can do second-layer damage.
Personally, I would advise against more engines at this point. Frankly, you will be much slower than likely enemies anyway, regardless of whether you are going 2,000km/s or 3,000km/s. So qualitatively there will not be much of difference: Either you outgun them and its good, or not and you are toast. Yet, pushing up the speed considerably means less payload can be carried and you would be less likely to outgun them in the first place. This goes unless you have a specific enemy with a known speed in mind.
