The Elements and their connections

[Anonymoose]

why the BLM and WHM have the spells they did

Conjurer once had all six elements, Black Mages traditionally have all six elements, and XIV couldn't really reconcile Conjurer turning into Black Mage, so when Thaumaturge turned into Black Mage and Conjurer turned into White Mage, they split the elements in a way that made sense - CNJ/WHM wields the powers of nature, THM/BLM wields the powers of ruin. There's little more to the division than, "SE did what they could with what they had."

It was a huge challenge <...> this is one of the times we just blew it up and weren’t able to put it all back together. It doesn’t happen a lot, but every now and then you just have to say, “Okay, we can’t explain this, and if we tried it would sound forced.” It comes down to the system, and you don’t explain them, and you hope people don’t notice, and then people notice, and they have this podcast, and I have to say…

Interview with Gamer Escape, Fan Fest '14 (Vegas)

As I said earlier, I keep hoping that they'll try to give both jobs their "full set" back in some form by LV99, but it's probably hope in vain.

Why the intial primal were Ifrit, Titan, and Garuda

This is all about which areas are (and are not) in the game and in which order you visit them.
The earlier you visit a region, the earlier you see what threatens it.

Phase One: Introductions
The early levels are spent in Thanalan, La Noscea, and the Black Shroud, which are under threat by the Amalj'aa, Kobold, and Ixal, respectively.

Phase Two: Cleaning Up
Of course, Limsa is also under threat from the Indigo Deep by the Sahagin, so once each of the introductory three cities has its fair share of thematic threat handling, you go back for Leviathan. And, also, of course, the Sylphs still live deeper in the Black Shroud, so you go back for Ramuh.

Phase Three: Moving On
With all of that out of the way, you can go on to Coerthas and fight Shiva.

Get your darksteelfoil hats for this next section, I'm about to make myself seem craz(y/ier)
I have no proof for any of this, it's just a suspicion I harbor based on a perceived pattern (that may or may not really exist). I think there was also a second layer to the primal order / area logic based on the fact that each region is associated with an element and members of the Twelve representing that element.

A Theoretical Pattern:
The first and last primals you face are in their element-appropriate region. Ifrit appears in Thanalan (fire), Shiva appears in Coerthas (ice). The second and third primals faced still represented the Black Shroud (earth) and La Noscea (wind) ... but backwards. Why? I think it was to make room for the others without breaking anything.

Dravania (water) and Gyr Abania (lightning) weren't in the game for the base version, which was all about the elements and the Land. One was abandoned and one was lost to the Empire, respectively, anyway, but that also meant that two regions had to double up on primals to make up for it. I suspect there was a time when SE had to shift it all around so it would make as much sense as possible, and that's how we ended up with the order we did. (They had to do the same thing with the stones of the Twelve, if you remember; some had to get shifted around a bit.)

The Sahagin (Leviathan) end up conflicting with Limsa Lominsa, which is the closest city-state to Dravania (water). The Sylphs (Ramuh) end up conflicting with Gridania, which is the nearest city-state to Gyr Abania (lightning).

For some reason that remains unknown to me (assuming I'm not just making all of this up and seeing patterns where none exist), they chose not to have the Ixal in Limsa Lominsa (wind) and the Kobold in the Black Shroud (earth). It would have made for a much more consistent pattern, in my opinion. There's even a volcano east of the Black Shroud for the Kobold to call home (granted it's currently extinct, lol). I guess the cultural lore just all works out better with them swapped.

The point, probably, is that 1.0 was kind of a mess and SE has done everything they can to make it all work.