I'm not going to argue whether or not the addition of the Wait function was the right way to go - but something DID need to be done. The fact that players could unintentionally Commence was a pretty clear design flaw. It's not just Gathering jobs that make use of the X button; you use it to target mobs, for instance, and engage auto-attack. Needless to say, targeting and attacking an enemy is not a rare occurrence in this game - particularly if you're farming FATEs with lots of targets.

Or how about the rarer, but extremely unfun case where you're about to talk to the Repair NPC because all of your gear is broken? Only - nope, you're in a dungeon now, and you might as well be naked...

The fact that the Commence window appeared and immediately became active means that players have a good chance of inadvertently entering an instance before they were ready. While this change may inconvenince folks who would like to select commence while afk, it really was the case that something needed to change.

Now, perhaps a better alternative would have been instead to add a one-second or so delay after the Commence window appears before the Commence and Withdraw options become selectable, while still keeping Commence as the default option. That way, folks sitting on the porcelain throne could still mash accept without going into "wait" mode, and players mashing buttons to select mobs or NPCs will have a moment's grace before they're sucked unwillingly into an instance.