I like the armory system to be honest, but all of the concerns voiced are good ones. But I'd like to put in my two cents as to why I like it.
First, not everyone has the time to devote grinding a class all the way up to level 50, and being flexible is more valuable in this game than in others.
Now I know people keep harping on the fact that once you get your job you never switch back to your class, but seriously...why wouldn't you take advantage of the fact that you can cross class all across the board? While the overall total skill amount is the same in the end (as you get 5 unique exclusive skills for your job, but have access to 10 skills cross classed) someone who understands the other classes can be incredibly versatile and useful in any role, creating a unique archetype that doesn't quite fit the initial mold anymore. However most people are far too lazy to do this.
The limitation on the weapons is also handy in that it keeps your inventory simple and straight forward for each class, but don't forget that there are class specific weapons now as well, things that your jobs can not equip. Just like you have class specific gear.
Now for all of the people (like myself) that have reached 50 with all of the classes, we are usually skilled in a handfull of these classes, but work passably with the others. For instance, despite having all of my classes to 50, I'm only really skilled as a Paladin/Dragoon or White Mage (or the classes obviously). This means that each person really still has unique skill and isn't based on equipment because equipment doesn't matter if they can't play the class well.
I have never got the knack for managing hate with a black mage >.>.
Something to keep in mind is that the armory system is sort of a guide book for the class to job transition. I mainly like it because it's basically like a specialized class, limiting what you can do within a class and giving you new abilities.
Anyway, I'm sorry I got so long winded, but I hope you can see that there are benefits to it as well! ^_^.