I can't give you a good justification but I can tell you with 99% certainty what the dev team thinks. I believe they think people are constantly moving merits around to suit their current job preference thus creating an infinite need for exp. They are actually right I suppose. I often move my combat/magic skill merits around depending on what job I'm playing at the time which requires me to save up at least 18 more merits. Uncapping ALL merits would create a finite need for exp unless they came up with something else to use it on. Inconvenience is not something a dev team should use as a tool to create a need to repeat a task ad infinitum and I would love to see everything uncapped but I'm pretty sure that's the reason it will never happen.