The armory system is fine, but they need to stop it robbing the individuality of classes. This can be done without tampering with that though.
Physical level is not fine. Some people seem to like god-moding on low level classes after getting a high rank (doesnt have to be 50, there are skill caps) but it just doesnt feel right to me. Furthermore, it's stupid that all stats are allocated from one base-pool as it kills customisation on an individual class level in terms of stat points.
The reward for levelling up a multitude of classes should be that you get additional skills and, well, classes. Not that you should have some inherited bonus to lord over newer players and make yourself feel special.
Finally, the current system is the reason why stats can't apply that much effect to characters, because if they did people would HAVE to stick to DoW or DoM at higher levels and crafting classes would rarely get stat allocation at all. Remind me again how that is enhancing customisation?
In addition, YOU are also not a game designer and therefore seem to struggle to look at the bigger picture, rather than just what benefits yourself.
Finally, suggesting that removing physical level will turn this game into a wow-clone is naive at best, and shows how little you know about the MMO genre as a whole. In fact, I fail to see how it's comparable to WoW at all in that respect, the fact you only use one character defines this game as entirely seperate experience in terms of progression.
EDIT: I've just realised, when you say the 'armory' system you're not ACTUALLY talking about the armory system (Skill assignment to different classes) as defined by the game, you're talking about wearing WATEVA PRETIS you find on any character at any time. This isn't the armory system, I'd recommend looking it up.
Besides that, no. The current optimal rank system for gear is really stupid and is totally killing people's ambition to level up because they can wear whatever they like whenever. There are reasons other games don't allow it, and yes, Kurikokaze was right these are the reasons the old team got scrapped.
So in actuality I disagree with you on both points raised.