There's a simple solution to your woe of 'what if I face an R: Thunder enemy' question. Turn off your Black Mage Job, and equip Stone/Stonera and Aero/Aerora.

Yep, suboptimal. Indeed, from what I can see, working as intended.

I have to say I personally find it very unfun for every single spell to be just a different-element carbon-copy of another and I like the way that the devs are going with the distribution of spells.

So why don't you try to find solutions more along the lines of what the devs are working with? You want all elements on one character? Alright, let's call that the Elementalist Job for Thaumaturge in 2.0, so we don't have to alter THM at it's base. You know we got ST damage on Thunder, AoE on Fire and Instant-cast Bind on Ice. Give me ideas for Wind, Earth and Water that are neither Single Target damage, AoE damage or Instant-cast Bind.

Edit: Also yes, making nighttime scarier is more important than giving more elements to Thaumaturge. Not nearly as important as a third DoM, however.