Answers

A lawyer is the first place to start. Your builder should be insured for problems like this. If it is a big box builder then I am sure something in the corporate contract has an answer for this. You definitely will want to keep any paperwork, emails, texts, etc just to back up your claim. Also the city/county should have the design on file because that is what the permit is attached too. 

Who made then the design change decission? Was it you that changed something and the seat was dropped due to the change? Or was it initiated by the builder? Did something else change that necessitated the eleimination of the seat?

If you requested a change that cause this to happen and missed it until the walk through the I don't see the builder as responsible. But if he did it on his/her own then I think they are accountable. In ether event there should have been a change order to document  the alteration.  

With more info about the cause and how it was initiated, if it was documented,if at all, would help the resolution to be much clearer. I can see responsiblity on both side. And a lot of greive and agreavation if laywer and courts get involved.

I would suggest arbitration as the next best course of action if you and the builder can't work it out between you. 

Are there specifications that say that there is to be a shower seat?

Contacting your local home improvement commission is your best recourse to start, since they typically have a fund to pay for a attorney for you if needed. They can provide mediation between both parties in hope that a court battle can be avoided. They will slso decipline the contractor if they side with you, and no contractor wants that on there record.