Some alternate qualities were intentionally chosen such that the "best case" may not just be geting as much quality as posible - while standard quality stats are intended to (at least almost) always be good to raise, the alternate quality system, since no-one has to use an alternate-quality gem if they don't want to, gave the opportinuty to experiment with stats that have more interesting tradeoffs, which appeal to certain segments of the playerbase.
The alternate quality stats were also considered in light of how they might interact with any potential future content that allowed getting higher values of quality on gems than are currently possible. It's cool when something new gets added to the game that makes people go back and re-examine some older things because new interactions open up.