Based on the currently known information about jobs, I'm going to assume that they will primarily serve to enhance the current class system. Let's break it down by looking at CNJ and WHM:

CNJ primary role (currently):
Buff (SS, Protect), Heal, DD. This is a great solo build because it allows for survivability plus damage. In groups, CNJ can be useful mostly as a healer and buffer, but can also throw out the occasional nuke if things are going well and mp consumption isn't a problem.
WHM Role (based on known abilities):
Buff and heal, emergency DD. WHM should have access to all of the current CNJ defensive spells (nukes might be taken away, as Yoshi-P at one point said there would be some limitations when activating a class). WHM Also gains Regen, Esuna (removes weakness), Benediction (huge AoE cure), Chainspell (rapid cures, quick raises), and Holy. Holy, however, consumes all of your MP in order to deal damage, so think of it as a last ditch effort to kill a mob.

Now, WHM abilities are going to be learned from 30-50, but there are a few mysteries that we don't know for sure yet.
1. How much access to other class abilities will be available when in "job mode" - this is huge. If you cannot equip any other skills from other classes, some people may prefer to just play as a class instead of the job.
2. What abilities do you lose when in "job mode" - while I personally feel this is a lesser issue, its certainly in the realm of possibility that losing a couple key class abilities may make the job not seem as important.

Final thoughts:
In the end, it will come down to the unique situation, the make up of the party, and the player's personal play style as to how these jobs will be used by the playerbase. I think once we get out hands on them, we'll learn that certain combinations of jobs with others in a party greatly increase the efficiency of the overall group. As a CNJ, I look forward to switching to WHM when in a group to focus on healing....those nukes on the left side of my action bar tempt me too much, lol. As for eliminating the armoury system once the job system is implemented, for the reasons stated above, it simply won't work. You probably won't be able to solo a WHM to 50, thus eliminating a much sought after (financially) casual player base. Choice and flexibility is the ultimate goal of any modern MMO developer, and as long as the don't put too many restrictions on the job system, it will be an awesome complement to the armoury system.