I guess it was done, to let the districts be more of a meaningful choice. While initially you would be better off building a research district; once you had enough building slots open, you would be better of tearing down those research districts and building more habitation housing districts so that you can place more research buildings.
Not being able to build luxury residences seems a bit of an odd; if you can place a factory or fortress in a building slot, it seems strange that you can't place residential buildings there as well.
I found out during my current play through that fortresses provide housing (albeit only 3 when upgraded), this did allow me to have maximum research output, with the addition of 54 naval capacity (3 soldier jobs * 3 naval capacity * 6 fortresses):
This is my default setup for habitats, and in my current game I have 13 of them putting out the bulk of my research and Naval Capacity.
BUT!, when it comes down to it, planets can be built as research monsters, take my Capital system for example:
About 5x the research of a habitat, all mining districts utilized, and while 15 city districts is required for housing, as a side effect it provides a decent chunk of trade as a result (and I've yet to fill the remaining clerk vacancies).
Assuming both the planet and habitats are in an already occupied system, the planet is more district efficient:
Koros: 23 Districts + 2 colony = +25 Empire sprawl (~1000 research)
Habitats: 5 * (8 Districts + 2 colony) = +50 Empire sprawl (~1000 research)
There is probably a few things that could be done (eg doubling number of jobs per district and habitation housing, have districts provide housing for the jobs, allow building of luxury houses, etc).
I also feel that the Trade district is pretty underwhelming when you miss out on the much more Trade/Amenity efficient merchant that you can get with Commerce Megaplexes on planets.
The Leisure district isn't too bad, but not really worth it due to the fact it takes up a precious district slot, and as shown above, you can get the necessary amenities with the Galactic Stock-exchange and a Cryo-revitalization center.
I still like the current incarnation of habitats, especially as they still retain the advantage of being able to get research immediately without having to wait for another building slot to open, and they seem to synergize very well with fortresses for additional naval capacity...but I guess they still could do with a few buffs.