I don’t understand this whole fairness debate, which seems to be founded on a misunderstanding of probabilities and is largely a function of the passive play on this site, which allows too many players to see flops and subsequent streets. The value of premium hole cards (even AA) diminishes with the number of players at every street.
Let’s take your QQ hand as an example. You stated that the big stack made a huge re-raise. Generally these types of bets (especially 3-bets) mean that the player is strong, and AK suited is indeed a strong hand. But QQ is also a strong hand, and probably worth defending in the big blind (that appears to have been your position since the player to your left was first to act).
Of course, I can’t tell you whether or not that you should have folded/called in this situation, because I don’t know the key details: for example, how huge was the 3-bet (this is needed to calculate pot odds), what type of player (e.g., loose or tight) is the re-raiser, what was the re-raiser’s position, and what were the relative stack sizes?
The underlying tone of your post, however, suggests that you sensed that losing this hand was inevitable (something was not right). The fact that the big stack hit a backdoor flush draw to win is irrelevant, since you were no longer in the hand. If you were in it, you could have prevented the big stack from getting there (which required running cards on the turn and river) by making your opponents pay heavily to see the turn card (I would shove here). Yes, sometimes people will call and you will get unlucky, but remember that they made a -EV play. People who consistently make -EV plays depend on luck to win and will pay you off in the long run, and that’s what you need to focus on, rather than short-term results.
The bottom line is this: while some people feel that the game is rigged, these types of beats can happen in “real” poker, but they tend to happen more often on Replay because people let them happen with passive play.
Pre-flop, AK suited is an excellent hand, and the big stack played it aggressively, putting himself/herself in a position to win by taking control of the action, forcing you to fold and isolating the short stack for heads-up play. This is precisely how you protect your holdings and reduce the probability of losing.