Regardless of what the original idea behind Merit Points was, this is 2015 and not 2005.

With the advent of the JP system and with content updates ending soon, there is no point in leaving restrictive vestiges of the past that were designed and implemented in a completely different gameplay environment.

Balance is not much of a concern and it hasn't been for awhile, since if you follow the trends within your own game you would know that for most jobs there's an optimal cookie-cutter set of Merit options the majority of the playerbase picks and the rest of the options are mostly a waste of Merits (with a few exceptions like SMN Category 2 for example). Same goes for most of the not job specific merit categories. Like it matters if I can merit a little extra MND on top of my INT, STR, DEX, options when most ilevel gear comes with stat-vomit, or if I have all Merit WS's at 5/5 when most of the time they are not the best options anyway even at 5/5. The only Merits that conflict with each other are the Emnity ones, if someone wants to merit both of them they will just cancel each other out.

All the removal of the Merit caps will do, is make us more flexible across different jobs and give us more stuff to do since most of us are sitting on capped merits most of the time.