Stellaris still does a couple of things clearly better than DW...
1/ Race customization and diversity. No doubt about it, still by far the king in this area.
2/ Exploration and the resulting missions and side-quests.
No, just no. Stellaris is only better at race customization because DW doesn't really has race customization. However, the pre-existing races of DW still offer more diversity in gameplay than Stellaris: None of the trait choices, ethics, governments or even appearence matters. It's all window dressing. Even hive minds or machine empires don't play radical different from normal empires. Hell, you can argue that hive minds are worse, because they don't have two mechanics (happiness and inner empire factions) that normal empires have. The only thing in race customization that really affected gameplay in a meaningful way was the different FTL-drives. Go figure...
And exploration and side quests? Well, kinda. Exploration is indeed the best part of Stellaris but in the long run, it doesn't matter that much because none of the stuff you can find is really a game changer. And the quests and missions are just glorified pop-ups, just like in EU or CK. They are mostly there to "shake things up" or to "topple the status quo". After all, we can't have the player have a trouvle-free time running their empire, THAT would be boring!! And after you have read them a couple of times, you simply skip over the text and click on the button that provides the best outcome, no matter how well written (read: full of references to better franchises that only TRUE scifi fans like us understand) it is.
Stellaris is an utter unsalvageable mess, developed by a bunch of incompetent people. Their only solution to fix gameplay issues is to throw in more numbers (consumer goods), to pile on more poorly thought out mechanics (factions) or, worst of all, gimping or flat out removing core features (ship design, ftl). It's kinda amusing how every dev dairy these guys have released starts with the phrase "I was always unsatisfied/unhappy/disappointed with..." But remember kids: "Stellaris is a great game and it will only get better! Paradox games are like fine wine, they only get better with time! (also more expensive but pssssh)"
Also, Martin Anward, Stellaris' game director, is kind of a dick.