I generally agree with this, but there's a lot of homogenizing going on currently. Cure/Physick. There's literally no difference. Why am I able to cross-class Physick as a WHM or Cure as a SCH? There are some cross-class skills from classes that you just don't ever take. Ruin? And some that are completely necessary like Swiftcast.
I don't really want to see a complete free-for-all when it comes to cross-classing. Don't get me wrong, I love customization, but balance goes out the window when you do that. I loved the subjob system in XI. I had a frkin blast as a WHM/DNC, dual-wielding hammers and Hexa-Striking the crap outta things. But it wasn't even close to a balanced game. There's no way I would have been able to do WHM/DNC in any kind of party, or current content. But it was fun.
The system in FFXIV doesn't currently allow for this kind of build. The skills/spells are built to work well with the classes they go with, and would either be completely useless or completely overpowered on other jobs. Not to mention you'd run in to the same issue where everyone would be taking the same abilities. All DPS classes would pretty much have to take Raging/Quelling Strikes, Blood for Blood, and Internal release.
I really think that one of the major mistakes that people make when talking about XI is assuming that it was a Trinity system game. It wasn't really intended to be that way, but at the time MMO'ers were mostly coming from Everquest which gave birth to the whole concept of the Trinity. When looked at in that light, the subjob system made a ton of sense. So called "Nonstandard" job makeups became an interesting addition to a team. It didn't really become "Trinity" until NA's started playing, insisting Ninja was a tank because it had an overpowered spell that made it evade all damage. :P
Unfortunately XIV is falling somewhere a little odd. It's trying to follow up with the sweeping success of WoW by appealing to an audience that's used to homogenized classes and easy-win gameplay, but a lot of the more faithful players are from XI which was decidedly more hardcore, and offered a lot more options for customization with ZERO homogenization. I certainly have no answer to this issue, but I trust the devs to make the right calls. They have a lot of input (Such as the article a couple posts back from this one), as well as player input that they DO follow up on.
Yoshi-P has stated many times that he wants to re-do the class/job system. That it's a relic from 1.0 that has no place in the current game. I actually suspect we're going to see this change sooner than we think. Please look forward to it? ;P