Here's the reason why I think that SE went with the Rogue>Thief route:
*Classes are the odd unconventional classes that Tanaka came up with to be different from the traditional FF jobs. (in 1.0, CNJ had 6 elemental tier spells plus Cure, Protect, etc. and THM had Banish(Astral/Light), Scourge(Umbral/Dark), and a bunch of enfeeble/dot spells and even an overpowered Cure+Regen spell.
*Jobs are the traditional jobs from FF that Yoshi-P wanted to bring back to make FFXIV have the FF feel again since Tanaka strayed far from it. Due to this, he had to make the original classes start to fit the role of their respective jobs. That's when the big changes to spells/skills took place. (THM got the traditional BLM spells like Fire, Blizzard, Thunder; CNJ kept Cure, Protect and Raise etc.)
Yes Thief is one of the classic six FF jobs but due to the class/job format, Yoshi-P had to rename it Rogue.
So...
*Thief>Ninja=X Why? Because Thief is a traditional job so renaming Thief to an unconventional class keeps up with the same format above.
*Rogue>Ninja and Thief=X Why? Adding two DPS jobs from the same class wouldn't really work since the DPS>Tank/Healer ratio is already high. DPS already have long queue times because of this as well...
*Rogue>Ninja=O Why? Rogue is basically Thief but due to the class/job format it had to be renamed. Also, people keep forgetting that waaay back in FF1, Thief TURNS INTO a Ninja so this is nothing new.
"But I wanna be a Thief! I don't want to use Ninjutsu and be a Ninja!"
*A big percentage of people who played Thief in FFXI subbed Ninja as their secondary jobs to have access to Utsusemi: Ichi/Ni and Dual Wield (Before SE naturally gave Thief Dual Wield) so it's probably going to be something similar like 17 traditional Thief skills from Rogue, and 5 Ninjutsu skills from Ninja. Also, you can always just glamour your gear to look like the green Rogue/Thief gear from the trailer.
Basically Yoshi-P had to recreate the game while still keeping the lore of the classes intact. So in order to do that, the traditional jobs had to be introduced as an evolution to classes.
Anyway, I hope all this would help people have a better understanding as to why SE went with this route. Yeah I was hoping Thief would be a job too but after digging through FF history and lore, I realize and understand why they did what they had to do and the pieces came together just fine in my opinion. ._.