I think... the skill changes in the next version actually go some ways towards this, actually. Interestingly, a lot of the skills work in a way where they provide a bonus that, while not quite split between the ships, is higher when you have less of a certain type of ship in your fleet. For example there's a "better flux stats" skill that has a higher impact if you have fewer combat ships (by deployment cost).
More relevant in the speed department, though: the "elite" bonus from Helmsmanship gives you the zero-flux boost whenever the ship isn't generating flux, rather than when flux is zero. So that alone would I think go a long way towards making piloting a Paragon more, ah, exciting.
That certainly sounds very encouraging, though even with the 0-flux boost and Unstable Injector, the blue murder donut is still too slow IMO. If I could swap out the Fortress Shield for Plasma Jets, I would in a heartbeat.
And - while this goes against the idea of having a small deployment - with the Coordinated Maneuvers skill, you could get (IIRC) up to +20% top speed if you have some frigates/destroyers deployed as support.
Yeah, but as you pointed out, those will just get blown up if they get deployed alongside a powerful ship against a large enemy fleet. Unless you hide them in a corner of the map, as Megas suggested, but then they might as well be buff ships that don't get deployed at all.
Also, bugger all plus 20% is still bugger all.
If that skill gave a flat buff, equal to all ships, it would be a different story, it would bring the speeds of small and large ships closer together (as if they were, y'know, coordinated). But as it stands it does the opposite, it makes the fleet less coordinated by widening the speed gap even further, which in turn discourages deploying smaller ships, because it becomes even harder to keep up with them to protect them.
That said - as Thaago pointed out - the Paragon is the slowest capital ship, really. Most of the other options have mobility systems, and are probably more suited to player use. Probably paired with the Paragon, to play anvil to your hammer. I guess my larger point here is that we shouldn't over-focus on the Paragon - it's a powerful ship, yes, but a lack of mobility is its main and pretty much only downside, so if anything could entirely counteract that, it would be pretty broken almost by definition. In fact, this is making me have some concerns about the elite Helmsmanship effect.
I don't think having a broken combinaton or two would be such a bad thing. It's a PvE game with a restrictive level cap that prevents you from getting everything, thereby encouraging multiple playthroughs with different builds. Finding broken combinations is where half the fun comes from in games like this. Perfect balance is boring, because there's nothing exciting to discover. And yeah, playing with a broken build will get boring sooner or later. That's when you retire that character and play a different build next.
As for other capitals, I just find them... worse, really, mostly due to being made out of tissue paper, comparatively speaking. They're alright and fun to fly against equal or lesser ships, but if I want to take on a couple Paragons or Radiants without swarming them with a ton of my own ships, I pretty much have to bring a Paragon of my own, since maneuverability doesn't help against those as neither can be flanked (the Paragon will just turtle up while it slowly turns to face you, and the Radiant has a better mobility system than you). So the only option is to slug it out, and non-Paragon capitals have neither the staying power to trade blows, nor the firepower to win before they've taken too many. If only there was a way for the player to, y'know, buff 'em a bit.
That's kinda the whole point of this thread. If you want to feel like you matter on the battlefield and aren't mostly just watching AI ships kill other AI ships, you have to have a small deployment. If you want to handle difficult enemy fleets with a small deployment, you need to use the strongest ships. If you use the strongest ships, the game becomes boring because those ships are very dull to fly. Hence the idea of buff ships, to either make Paragons faster (= more fun) or to make the other, faster and more fun capitals stronger (= viable in a small deployment). I guess you could say my dissatisfaction is a case of a player optimizing the fun out of a game, but then I'd counter by saying the most optimal way of playing a game should also be the most fun.
(The Doom is a personal favorite of mine, btw. It can be super powerful; I think you might find that if you pilot it alongside a Paragon, it could make for an equally effective combo as Astal + Paragon.)
Eh... I have an irrational hatred of phase ships. Sorry.