All sentences hold the same meaning, and differ mainly in their execution. The reference sentence, "You don't get everything you want," is best in terms of fluency/native use of the phrase, while (1) and (2) appear to lean towards what one would call a proverb (e.g. fancy advice).
For instance, if we add the contrapositive phrase to (1) or (2), we get this:
"Not everything you want, [do] you get, and not everything you get, [do] you want." In essence, a piece of advice heading listeners to have reasonable expectations about their wants and procuring them.
Use of "do" or not in this case is a bit more... aesthetic? I would argue that inclusion of "do" make be closer to a full sentence, but removing it (like in (2)), creates a more concise and crisp proverb-like sentence structure when compounded with its contrapositive counterpart.
All in all, the reference sentence is best for fluidity and terseness, while use of (2) in tandem with its reverse is best for doling out some advice (perhaps a bit Yoda-like, as HammerN'Songs noted).
Hope this helps, and let me know if further clarification would be useful!