I like the organizations. One thing is that organizations could themselves be builders. (So each planet handles its own build queue and decisions, but the presence of particular guild can influence their progress and decisions. A space elevator might be a pipe dream for a provincial backwater planet, but the existence of the Skyhook Guild brings it within the realm of possibility.)
I'm thinking of the guild of hydrodynamical engineers that went around Europe in the Middle-Ages (-ish) to build canals and such. It wasn't that each city would have a hydrodynamical guild; there was just (if I remember correctly) one and they traveled where they were needed.
So if the goal is to have some control over whether your empire builds a lot of fuel depots vs. universities vs. whatever, you could do it by chartering organizations that build these. You just know that they're out there doing their thing, and doing it better than the planets would manage to do in their absence, but you as the emperor don't necessarily know or care where. At the point that you have 200,000 planets, they might be founding a new planetary university every week, but you don't have to be notified except regarding the big picture.
Also, it gives you something to have audiences about. Organizations would have liaisons in the emperor's court, and that lets them potentially beg you for stuff, get into fights with each other that you have to adjudicate, etc.