As much as people may want Carbuncles back, there are also people that prefer their faeries or just a general dislike of pikachus.

So you want them to please you and piss other people off, kay.

As for the class system, the benefits of the soul crystal outweighs the extra cross-class skills - especially alot of the cross-class skills are weak unless it is enhanced further by a trait later on. Unless the system gets completely revamped, I don't think it is going to change. As for your suggestion of having classes able to ignore game mechanics is pretty laughable as it is going to take away any difficulty of the game that is already designed for casuals.