SOTS has a few things better than Stellaris and vise versa.
From what it looks like:
- Stellaris has a race generator for a more roleplaying experience where it is far more flexible than SOTS which has 8 predefined species.
-SOTS looks like it has a better tech system with a large predefined tree which adheres to its strength in ship combat, its less dynamic than Stellaris, but different races have different chances for techs.
-SOTS appears to have a more specialized ship system where the mission section defines the limits this ties in with the points above as SOTS is less about empires and more about conquering the map.
-SOTS has firing arcs and better tactical combat with the specialized ship sections, while Stellaris (Does this have firing arcs?) appears to not have firing arcs and has a more generic molecule system, but you can specialize just as well if you want I reckon.
-Stellaris has a far more developed diplomacy system and resource system, but SOTS has a better Trade system as you can raid and defend trade routes
To summarize, Stellaris has similarities with SOTS but it focuses more on being a space empire and diplomacy while SOTS is all about ship combat with a sprinkle of empire management on a strategic and tactical level Although lots is improved in A Murder Of Crows (AMOC).
However, keep in mind that SOTS is from 2004-2008 ,going by the expansion packs, ie in the golden age of vidya while Stellaris is a long awaited Space game during the miserable dark ages for 2007 onwards.
EDIT: Zaaldar, While they look the same, I think the modules dictate the amount of specialization in Stellaris, I won't deny that they are not similar however. Probable inspiration there.