I absolutely agree with 1 and 2. I do not, however, agree with 3. Warning: wall of text with long explanations and recommendations incoming.
Cisterns as a means of water storage were used as early as 4000 BC, and as a system of drainage/early sewage around 500 BC, so coming any later than the Classical era wouldn't make historical sense. Really, they should come in the late Ancient era for historical accuracy. Which would be fine as no one would ever build one before then anyway.
I would actually consider moving Cistern forward to Irrigation or Masonry. Yes, it's even earlier than Engineering, but:
- It's more historically accurate (and you would need to utilize cisterns for neolithic era irrigation, or stonework to build them in the first place)
- It forces you to make a decision and actually try to get it. Engineering you're always going to get. Irrigation and Masonry may not be things you get right away. So putting Cistern in a less common tech adds an (albeit small) amount of strategy and decision making to its acquisition. Acquiring the tech may be an opportunity cost in itself depending upon the game.
- Cistern being available earlier is irrelevant as far as balance is concerned because you likely won't need to build one until late Classical, regardless. So the only effective way to occasionally delay it is either have it somewhere grossly historically inaccurate (late medieval) or have it in a less common tech that isn't always immediately acquired (such as Irrigation or Masonry) with a higher production cost. But as I explain below, I think it should be available when you most need it (late Classical/early Medieval).
I think the problem I described in my first post is solely Sewers being so high in housing. I'm of the opinion that viable housing options should be available if you choose to pursue them, and that each housing building/upgrade has its own identifiable niche. Cistern helps fill that early-mid game gap where you would normally feel like you have to spam builders and farms in your bigger cities just to keep up on housing, which is frustrating and not at all fun gameplay. If Cistern doesn't fill that late-Classical to Medieval housing drought, I don't see it as having a niche or being necessary. My only problem with Cistern+4housing Sewer is that in combination they make the dedicated housing district irrelevant in all but the largest cities, and only in games that probably should have already ended by the time you build them.
I have two proposed recommendations for your next build.
The first contains mostly simple reversions:
1. Move Cistern into Irrigation or Masonry for historical accuracy and to force the occasional opportunity cost for acquisition (I like Masonry)
2. Reduce Sewer's housing back to 2
3. Return Sewer back to original price
Alternatively, my personal recommendation expands the niche of the Cistern and Sewer. This proposal makes them slightly more culturally accurate to their roles in history, as well as making them slightly more interesting/utilitarian:
1. Move Cistern into Irrigation or Masonry for historical accuracy and to force the occasional opportunity cost for acquisition (I like Masonry)
2. Increase Cistern's amenities to 1
3. Reduce Sewer's housing to 2
4. Increase Sewer's amenities to 1
5. Set the cost for both as appropriate
This yields:
Cistern: 2 Housing, 1 Amenity, 100 hammers (same base price as aqueduct)
Sewer: 2 Housing, 1 Amenity, 500 hammers (approx 25% increase from base Sewer)
These changes have both historic and mechanical justification.
Historically, sewage and plumbing are certainly as much luxuries and quality of life improvements as they are logistical ones. I don't think I need to point out how dirty and disgusting societies without some form of sewage system are. Needless to say, not only does housing and health improve with sewage systems, but people are certainly going to be considerably happier when they're not literally living in their own ****.
Historical Example
Mechanically, having hammer costs inline with equivalent districts/buildings will make the Cistern an opportunity cost investment that will require more delicate timing and more consideration than just spamming it out quickly and cheaply. It does become better than the aqueduct in a city that already has fresh water, but that does make logical sense. In a city where you already have ample fresh water, what would be more beneficial: a functional-but-primitive sewage system, or more fresh water?
This also allows you to place it earlier in the tech tree, such as in Irrigation or Masonry as recommended above, without worrying about it being built too early due to being fairly cost-prohibitive in the Ancient/Early Classical era. At 2H 1A for 50 hammers vs Roman's Baths of 4-8H 1A at 25 hammers, you can see it's still pretty costly, but gives everyone an early amenities option without stepping on the Roman's Housing+Amenities niche. As can be seen, Baths are far superior to this version of Cisterns, not to mention the fact Romans can (and historically did) build both.
The Roman/Carthaginian cisterns, plumbing, and aqueducts were very elaborate and luxurious pieces of architecture that were an incredible feat for the time. I feel that should be reflected by their in game bonuses and construction time.
"The extraordinary greatness of the Roman Empire manifests itself above all in three things: the aqueducts, the paved roads, and the construction of the drains."
-Dionysius of Halicarnassus
Sewers now provide +2 housing and +1 amenity. I've also added a third tier to the chain (the Water Treatment Plant) which you get in the Atomic Era. 
Whenever it first appeared, it seems appropriate that it end up at pottery, and now it is! 
