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I mean: It's basically the same as the Eclipse-class just 2km shorter. Why not just build another Eclipse?

Economy. Dark Empire had a fraction of GE's resources and in mass production, this 2 km, simpler design and less intimidating look made it possible to, for instance, make 20 Sovereigns instead of 15-16. That's 4 star systems more to completely overrun with this ship. Eclipse was meant to be the flagship and an icon as well as the unstoppable juggernaut, you don't need more than one of those, when Sovereign in an actual confrontation is still unbeatable for most planets and regional fleets, and even 2 Sovereigns more means a drastic change in the pace of the war.

It's like in the industry. Saving 2000 dollars on each fighter built isn't much, but when you build 5000 F-16's, it suddenly means 10 millions dollars saved on the production.