One thing to remember is that the acquirer has probably done this before while the acquiree is a first-timer. The details are almost certainly going to favor the party with the most experience.
I once worked for a company that was acquired. At the first all-hands meeting after the acquisition closing, the CEO was practically gloating about how cheaply he was able to get us. All because he knew how to structure the deal in a way that wasn't transparent to our company owner.
If there is one way a small shareholder can ensure that they are going to be treated well it is to see to it that they hold the exact same kind of stock as a much larger shareholder. That way a bigger fish will fight for your rights with a lot more power than you ever could do by yourself. There are then still quite a few ways in which you could be screwed but far fewer than without that precaution.
I once worked for a company that was acquired. At the first all-hands meeting after the acquisition closing, the CEO was practically gloating about how cheaply he was able to get us. All because he knew how to structure the deal in a way that wasn't transparent to our company owner.