If I had to hazard a guess, I would say it's kept not just because of the huge amount of tinkering needed under the hood to do so while still keeping the system workable, it is probably also required for the benefit of 1.0 players who have yet to rejoin the game, and could use their old 1.0 character data, which would still retain the 'class upgrades to a Job', and furthermore, retain all their previously attained EXP from 1.0 - so changing classes into full Jobs from level 1 would potentially cause errors in the data that SE probably want to avoid having to fix, and prevention is better than cure after all.
Also, another point needs to be raised - changing it would make the GUI neater, but at what cost? SE would have to scrap all the class quests, and have to make new 'from level 1' Job quests for the starting classes which just violates the lore in so many ways. It would just be too much of a can of worms for SE to bother with, with little overall benefit.