I've tried out habitats and found them a little disappointing and mildly annoying. Disappointing because they had a fairly weak output compared to even small planets and annoying because I could relocate 1 pop away every few months for some added micromanagement or halt growth when full, lose the +25% pop growth from the food decision, take a -% total production stability hit and have some of that growth lost when my ecumenopolis hits the immigration cap of 5. So I'd be paying with pop growth twice and total output once for a little less micromanagement (and less energy spent relocating)... and I still needed to relocate robots anyway.
Habitats seem better for wide play and xenophobe slavers than for xenophiles (who struggle to unlock all the building slots while slavers do it easily). That feels a bit strange to me because I'd like a Babylon 5 type station at some point and the 100% habitability seems to encourage egalitarian xenophiles with migration treaties to use them... but they'll be less efficient. It's also very gamey - unlocking building slots with battery farmed livestock put in military strongholds to avoid having to build housing really does seem like an obvious exploit to me. Especially considering habitat military buildings were nerfed/separated once before because they weren't supposed to be as good as planetary ones. It's amusing to imagine the situation in your empire but it is an obvious exploit/design oversight nonetheless. If the extra building slots represent spaces used by the additional workers then the number of chickens shouldn't really influence how many refineries you can build (except indirectly by how many people you can feed). Nor should a habitat open to attack from all sides be more defensible than a planet with underground bunkers shielded by miles of rock.
For the oddity of the current situation picture a cartoon where an empire has a series of habitats each with 5 refineries and it encounters the McDonalds habitat which has 10 refineries instead. They want to learn the secret. They look around, the exact same number of workers (but all employed rather than some unemployed), same number of beds... what could be the difference? What is their secret?
Answer: Thousands of Sapient Chickens under the floors being made into McNuggets! (Bonus points if they each wear a little metal helmet and have a rifle strapped to them to represent the strongholds)
But I can understand it's fun to find a more powerful or efficient way of playing even if it's a bit of a grey area if it's an exploit or intended strategy. In my last game I was filling habitats with livestock to unlock all the buildings very quickly and also filling the Portal Event planet with livestock to unlock several additional portal researcher jobs and using them on other planets for the extra merchant jobs. So I can see how fun and useful it is to pump up your population numbers when you have thresholds to meet. It's a tangent but personally I'd have 0.25 housing using livestock/slaves count as 0.25 people for unlocking buildings, or have them not counted at all if they're working uncapped jobs... or count less based on their living standards - so social welfare unemployed still count as 1 pop but chemical bliss unemployed count as 0 (Not final numbers).
Anyway, I liked the portal research planet because of the planetary feature and the 1 job per x pops mechanic... and livestock/servants are fun because of the uncapped job mechanic making them far more flexible and useful. Habitats aren't fun because they lack unique buildings, have sad districts, have no features and are relatively expensive in terms of time, influence, alloys, perks etc. So after all that rambling, what would I do?
Personally I'd have the following:
1. Pops have less efficient housing useage - all pops cost 1 base housing for all strata (oxygen, life support etc. needed even for livestock/slaves), 0.5 for robots (no life-support needed - also a buff to machine empire habitats and a needed buff to robots/droids/synths).
1.1 Limit the extra sources of housing by making a replacement stronghold with different stats:
"Officer Training Facility provides +1 Cadet Job, +5 naval capacity." Upgrade provides more cadets and a soldier job.
1.2 Carefully consider the balance before adding special housing building. e.g. add an alloy cost to them but increase their housing benefit significantly so you have a choice between added sprawl via housing districts or high expense + upkeep but no sprawl increase via custom made habitation domes.
2. More efficient districts - more jobs per district or scaling jobs. e.g.
Trade districts also add 1 Merchant job per 50 pops.
OR Trade districts also provide +1 Merchant Job (Science Director/Administrator jobs)
OR Trade districts also provide +2 Clerk jobs (Researchers, Leisure jobs)
3. Constructed Features via Decisions. Adds jobs per x pops:
Physics/Society/Engineering Research Hub - 1 Research job of the appropriate type per 20 pops. (Would also scratch the itch of players frustrated by the inability to focus on engineering or physics research - myself included)
Expand habitat - has 3 levels, unlocked by master builders. Each has an influence cost and adds to the district cap.
Features require an initial investment but are permanent and without upkeep costs but lock out other features unless removed via decision.
3.1 OR Add events that would allow you to connect with the habitats a little more - borrow from Babylon 5 with some references to it or to other science fiction habitats. Events could make habitats feel alive and unique, with different paths and outcomes for xenophobes and xenophiles, spiritualists and materialists etc. The end result would be added features like the above idea, just more variable, less reliable and more surprising.
4. Add Habitat specialization - but instead of +5% to researcher jobs like tech planets this uncaps jobs of a type. E.g. A Trade Habitat would then have uncapped clerk jobs, trade districts could then provide smaller numbers of merchants instead of clerk jobs. Needs a decision to confirm the specialization. (Allowing investing heavily in fewer stronger habitats rather than many weak ones i.e. tall instead of wide spamming of habitats).
4.1 OR Allow normal specialization like planets but perhaps give a larger bonus to habitats (+10% instead of +5%). (Mostly just so they get the name in the outliner and a slight boost to output).
5. A cost reduction for Tall play:
Influence and upkeep costs for habitats is increased by empire sprawl +1% per point over. Base influence cost for habitats reduced to 150 and base upkeep reduced to 3 alloys. (Discourages spamming habitats as each additional one will have slightly increased costs but also allows the first habitats to be built sooner and gives a strong incentive for use when under or near to the admin cap.)
6. Unique habitat decisions:
Uses for rare resources (NOT matching the planetary pairings where gasses = science) so:
Exotic gasses boosts civilian trade speed,
Volatile motes boosts science by high energy experimentation and reactions
Crystals boost alloy production via laser enhanced production techniques
(Since they aren't using crystals for Commerce or Gasses for Research some other use for these resources would be interesting... the other option is special buldings but this requires less work/art).