As someone who has not been there and has zero experience in this, I'm left wondering whether you had more leverage to ask for "X,Y, and Z" before the deal closed. Not from the acquirer (avoid risking the deal), but from your employer. Surely if you explained the situation and how it is relatively unfair from your perspective, they might be able to negotiate on your behalf?
At any rate, the relationship deteriorated, which is not uncommon when a company is being bought or sold. We kept our smiles on until the acquisition was complete.
Have you participated in startups since then? Did you take any extra precautions after this experience?
I have been involved in start ups in two ways in the mean time. First, I have built up and sold my own small start up. This was much easier though as I was the sole owner and employee. Throughout my time building it up I did occasionally hire contractors and consultants on a 1099 basis. Overall, this made selling the company and assets a whole lot easier.
Second, I have worked for start ups, quite a few actually. But at this point I actively will not take an equity stake in any start up I work for. I always work hourly and get paid my standard rate for any work produced. In this time I have been involved with two start up sales. They were much easier on me, the owners, and the acquirers. Basically, I had been paid all along what I felt was fair so I didn't try to get anything out of the arrangement as it was being sold. I could be very focused on the owners best interests and not my own. In the end, both gave me substantial bonus amounts for my help and trouble and we all walked away happy. I also contracted with both of the acquirers after the fact in these cases. Again, everyone was quite happy.
One thing you must understand about the sale of a business is everything is very quiet because everyone is afraid of being screwed over. The company you work for wants the sale to go through and to have their exit be fruitful after many years of work. The company buying your company would like to get all of the assets, of which you are one, and make the new entity profitable for them in some way. You want to be treated well and see an exit that you believe you deserve, and so on. This is a tough balancing act and unfortunately, not a situation most people treat very honestly. I was there! I know how you feel.
What I did was stayed until the documents were signs. I was officially an employee of the new company for one day. The companies were officially (from a legal standpoint) merged. I then went to my new bosses and said "Now that the companies are merged, I need you to make this right for me by giving me X, Y, and Z." They said, "No way, you have a job, get back to work." I then packed up my stuff and left to one of my other job offers. I got what I wanted. The company I had worked for got the exit they wanted. The new company wasn't very happy but never the less got the merger they paid for.
At any rate, your milage may vary. Situations like this suck! But remember deep down this is business. Do what you need to do to make yourself and your family or whatnot comfortable and happy.