I do see a lot of suggestions concerned with Paradox and although they have released some great games I don't see them as being much better than CA. For example I'd be gutted if CA took on Paradox's DLC strategy, core mechanic and a few graphical touch ups. Don't get me wrong I like the look of some of the big expansions of one of their many grand campaigns.
One game that does look quite interesting is Stellaris, although I've only been interested in historical from the playthroughs I've seen it looks like a great game and some of its ideas could translate well to TW games.
One is the major constructs and advanced tech. I think this is something lacking in TW, something that takes an age to build but the advantages are well worth it. In terms of advanced techs (or ascension perks) this could be something that takes your faction in a particular direction be it, diplomacy, trade, military etc.
I think this would help the late game and allow a final huge invasion, while the major constructs and techs allow you to fight a final invasion by Chaos. This system could allow for a ladder system so how well you fight this final invasion is scored and assessed.
I realise that the late game is just a case of painting the map blue/red, so it would be nice for something positive to feature rather than creating higher difficulty through random invasions. The point of the early/medium game is to prepare for the final invasion, which expects the player to have domination over the map.