I think the method is sensible, in some ways; a DLC allows more leeway in development than the base game, and it needs a unique selling point.
But sometimes, those unique points end up being imperfect. Scrapping those seems reasonable.
On the other hand, removing things like retinues entirely and then adding them back in in a DLC would be sad. And we know at least the Way-of-Life improvements aren't scrapped.
Something like Merchant Republics falls a bit inbetween - in my mind, they never worked perfectly, so not putting them in fully fledged might be possible and leave a cleaner base to build them up properly in a DLC or expansion... but on the other hand not having them at all would feel like a step back, so implementing them imperfectly could be better than nothing.
(and remember, despite no DLCs, CK2 did narrow down content from CK, thereby allowing the base game being improved).