They are not identical as you have the module slots distributed differently.

But I agree that they are very similar.

Not what you had in Endless Space 1.

But I think this will change in future updates and I expect we will have unique modules for factions or maybe unique bonuses to ships like in ES1 that will make the difference.

Thanks for the hint, but I've read through that one and I feel it doesn't cover what I would like to know which I maybe have not done good enough of a job to convey.

I want there to be a difference between a Cravers carrier and a Sophons carrier and a United Empire carrier, and so on. It seems to me that if you equip them with the same equipment and upgrades, they will be completely identical. Is there no way to mix it up a bit? Could there be different modules available for the different races ships (or maybe there already is?), could ships have some other abilities outside of equipment that is given to them just because they are ships belonging to that race, does every race last, and biggest ship have to be a carrier class? How about the Sophons have a support type end tier ship and so on. Could some of them have a titan class ship? I know this would mess up balance, but I'm just tossing out ideas here.

There was such a unique unit line up in Endless Legend between the factions, I'm kinda disappointed not to see it trending in Endless Space 2.

There's already a thread about this, search for "Starting Ship Balance".