I've been wanting to post about your starting Flagship for a while.
It's far too OP from the beginning. I would assume this is WiP, bigtime, though. But it still needs to be said, because...
Humanity's VERY FIRST FORAY into space (your flagship) is, from-the-get-go, AN ABSOLUTE star-destroyer. Able to keep up with the most incredible ships from empires thousands/millions of years old. It's simply not *dangerous* feeling.
Now, I may be the only person on earth who's like this... but my absolute favorite part of any RPG - is when you start at level #1, with rags and a rusty sword and shield. The first time you actually get a sword made of iron?! RPG Heaven. And then I quit when I have full ebony armour and a fiery glass sword that makes you invisible when you're standing still. When I can't get any better, I'm so done. I actually... this may be heresy... but in my 10 replays of Star Control II, at least 4 of them have ended when I got the Hellbore and trackers and maxed the turning and thruster modules. That should be the end of the game, right there. I see it as there's nothing really left to do. SC2 didn't do a great job of spreading out the upgrades, so that NOW when I play - I go straight for the BIO units up front, and upgrade everything right away. A few months in, and I've already basically "beaten" the game. This needs to be crafted specifically to stop you from getting too powerful early on. And a big portion of that is hard counters to earth-tech.
In the build I played, I felt like all that was just given to me at the very start of humanity's first jaunt into outer space. I agree that there are no real counters to these insane nukes, coupled with the speed and turning radius of your ship. I want to start way, WAY before any of that.
But to IBNobody's point - if you view your flagship as arms and armour in a typical RPG, the extension of that should be that the SHIPS in your repertoire need to be your early arms and armour as well, before the upgrades come. So, in Baldur's Gate, a fiery greatsword would be perfect for fighting humans, and a lightning wand would be needed to fight a slime... in Star Control, a Spathi should be used to counter a Mycon, and a CHMMR should be used to counter an Urquan (but not a Kohr-Ah). You usually can't do everything yourself in an RPG, which is why you get a party. Ships are also your "party". Play a mage, you're still going to need a tank to get the beating. We need this synergy to encourage varied gameplay BEFORE you get any upgrades to your flagship.
He's got a good plan, which... it pains me deeply to say about @IBNobody.
Placement of races was key. Does anyone think it's a coincidence that our closest neighbor was the only ship that could outwit our initial homing missiles?
Ship counters was key. You NEEDED Spathi, and it made losing them so much more painful.