I haven't fought the Royal Armada for ages, but yes, the key tactic to the Armada and to Valkyrian ships in general is to separate them. And against things like the capitals, either weather the storm or kite them from range with weapons like the Gauss Cannon. The flux dissipation on the Vatican family is abysmal, I tried using a Vatican III with missiles as the primary weapons and all medium/small slots using IR-PD and Quad MGs plus 50 vents and 50 cap, still totally unable to handle it's flux. The IV is not much better. A lot of Valkyrian ships are incredulously slow and move at like 10 meaningless-units-of-measurement/s. If you can put an Injector or Aug'd Engines on a capital, you can keep distance from them pretty well. Pick off the cruisers (because they're like vanilla battleships) and destroyers. The Yoshura has better flux dissipation (when you're flying it with 50 vents) and the Yoshura II can be nearly immune to flux issues (I used mine with maulers in EVERY medium and large slot). Not to mention the Yoshura II's ship system which makes an assault nearly pointless unless you can alpha it off the field.
As for a playthrough, my playthrough started off in Exerelin (where dying isn't much of a punishment in the beginning because free faction frigate replacements) with getting a Yuusha, then several Yuushas (5 of the suckers) then moving into one of the Nirvana types before settling in a Yoshura for quite a while. I've since re-appropriated a Neutrino Banshee-Norn and I use that. I never found much use for the fighters because most fighter wings throughout my playthrough have been the flying guns, the corvettes. The Jenova never seemed like a good ship to use, the AI doesn't have much problem with lack of view range like my own ship does when rebel Jenovas are on the field. IR-PD > IR-PD lasers, every time. No worry of running out of charges and will spray down fighters unlike the laser which is dedicated missile defense. A good weapon of choice on a lot of Valkyrian ships is the HI-IR laser cannons. Long range, coupled with fairly low flux usage and good DPS, making for excellent stand-off weapons on AI ships. I have yet to see an Ether Driver, those seem to have turned into superweapons or something on my playthrough because all three Valk stations have not had a single Ether but are stocked with entire stacks of most other weapons.