I don't think the part about 25% of the mechanics is true. They even dragged some mechanics that felt like expansion features (like adding Chinese factions instead of creating a system that would hit China especially hard). They are changing the core game all the time and there is that problem of them adding new mechanics instead of refining old ones. They added autonomy and then added corruption that is functionally the same thing but on the global level and thematically doesn't fit at all. They have stability, prestige, reputation, power projection, legitimacy, unity and god knows what else - and all of this stuff is interchangeable and thematically pointless (imagine a country with great stability but without legitimacy, or with low prestige but high power projection and reputation). But even the bigger problem I see is that all the mechanics added in DLCs are either solitaires for specific countries (You don't care about Aztec DOOM or republican factions or revolutionary factions or Prussian monarchy or Ottoman monarchy or Coptic reforms or Indian religions etc unless you play as those specific factions) or are disjointed things that add some rare effects (Estates, Parliaments) that do not have an affect on other stuff - because you can't have a really important feature as a DLC and still mantain core game even remotely balanced.
Still even with all of that EU4 may be my most beloved game ever, even if I have doubts whether release patched version was worse than the current version would be if you turn off DLCs. They used similar policy with Cities Skylines and there it worked much better AFAIK.
And if EA or Ubisoft had published Pillars of Eternity you'd have Eder as 1st day DLC (Follower of Dead God DLC, given for free with pre-order) and would have to find collectables all over big empty maps to unlock crafting recepies and books. With Bethesda it won't be any different but wouldn't properly work for several patches and have fun exploits left forever.