This is a really good question for any person going through the process of having a home built. A lot of your problems are not out of the norm but really illustrate why it is so important to go to the site a few times a week and walkthrough and take pictures. I cannot stress this enough.
Let's talk about your OSB subfloor.
OSB is just pure crap for a subfloor, especially with one with joists more than 16" OC. It is a much cheaper and easier install so builders love it. I don't care what the OSB specs rate it at - it is flimsy material that can't take moisture or blunt contact well. I mean I think they rate 23/32 to be installed on 24" OC which might be what your joist spacing is (what is the distance between your joists?). I can tell you unequivocally that me being a little more than 200 pounds can jump right between two 24" OC joists for a 23/32 OSB board and crack it - been there done that. This isn't a tangent I am on. I am telling you don't replace this crap with the same thing and expect wildly different results because of "water damage".
Water damage is real for the OSB subfloor boards and your joists. If your joists have water damage I don't even know what to say. Depending on how bad it is they may need to be take out which means any wall above may need to be removed (swelling will cause tension and unlevel expansion - slanted floors and walls). This is pretty extreme but I have seen it. As for the floors yes water damage causes OSB to become brittle and expand in places.
Given #1 and #2 and the amount of places that are "soft" I am really doubting that the OSB was thick enough and/or installed correctly. OSB should be installed using T&G or blocking. It should be perpendicular to joists. This controls some of the deflection and movement.
Talking just about the subfloor. The water damage in my opinion didn't matter long-term. Long-term your flooring was eventually going to have these soft spots - within 15 years. The water damage just sped up the process of exposing an unsuitable product for its application. I am fine with OSB + 1/2" plywood. But every single home I have been in with joists greater than 16" OC and only OSB I could tell by walking on the floor in less than a minute. I mean let's just say you had a 300 pound friend over and they were tipping to put a shoe on - your floor could crack. Ridiculous.
Lee Sam has a very good answer and I would follow his advice but I would even more so put pressure on the local inspector. As a homeowner - not a contractor or builder - I honestly would be quite aggressive with the inspector. Let him do his job, see what he has to say, but someone in his office really f'ed up and if you aren't aggressive they will just end up covering crap up in cahoots with builder. I would not just push building codes but this is a safety concern. Local city and builder would get sued if someone was seriously injured falling through a floor.
I would ask inspector to condemn the house (more on this later) for safety reasons until the floor gets fixed. I would demand that the house is retrofitted with 3/4" plywood. If the builder refused I would have contractors out there doing it and bill the builder. If he is still building townhouses near you it is very easy to walk around, take pictures, and put leverage on builder by going over your issues with the other home owners.
If your subfloors are bad you cannot continue living in the house. The subfloor literally affects almost everything in the house and if there are issues with it then you could be spending a lot of money in the future fixing non-subfloor items because of the bad subfloor. Let's say that someone says you need to add a 1/2" of plywood to fix this... Well all your doors have to be cut, tons of trim work needs to be redone, cabinets may need to be moved which may affect plumbing and electrical, tile work may have to be totally redone. That is just the starter list.
Also there is no way in hell I am letting some builder open up ceilings to put in cross blocking to keep subfloor from deflecting. This is nonsense. Yes it will help keep the floor from deflecting to a point but it is not structural and not tied to the subfloor well enough. It means that your subfloor will deflect but just not as much (until the blocking loosens). A builder suggesting this means the only thing they care about is getting your home "good enough" in their minds until warranty is out. When the builder suggest putting up the blocking I would ask... "So I can tile that area once you do that and it won't crack?" He won't say this out loud but to himself "Of course you can't be the subfloor is still spongy and messed up."