I was just thinking about how the Dragon Quest games are actually not typical JRPGs. Usually, in JRPGs you play as a predefined protagonist, but in the Dragon Quest games, the protagonist is meant to be a representation of the player. (DQ3 did this the best, with DQ4 also being decent, but IMO DQ5 didn't do it so well, but I digress.) DQ1 is even more atypical, with its open world structure and mechanics like needing to light dungeons and keys being consumable items, which you don't generally see in WRPGs.

Then the Ultima series isn't typical of WRPGs of its era. You have games like Wizardry, Bard's Tale, and Might & Magic, which built off each other, but then you have Ultima, which pretty much did its own thing (at least until other WRPGs started copying some aspects of the game). In fact, I see more early Ultima influence in JRPGs, with the world map and Phantasy Star 1 having first person dungeons just like Ultima 1-5.

Furthermore, we can also look at 2D platformers. Most NES 2D platformers give the player character a weapon and a health meter; Super Mario Bros. does neither.

Of course, no post I'd make on this subject would be complete without mentioning the SaGa series, which is extremely atypical. SaGa 1-3 (though less so for 3) are linear but have unconventional character growth, while the Romancing SaGa games straddle the WRPG/JRPG line.

So, any other examples, preferably for genres I might not be so familiar with?

It's kinda weird that you pick Ultima and DQ as atypical examples of their genres when the genres didn't even existed before they came out, don't you think?

Besides, with how fast gaming evolves, saying something is "atypical" can only last for a few months. Saga's leveling systems are similar to The Elder Scrolls, and takne from FInal Fantasy 2, so it's not like they made that up, or you don't have similar examples.

DQ is a good example.

I think Fire Emblem would count also for the Strategy RPG genre. I actually have difficulty playing other games like Tactics Ogre, Final Fantasy Tactics, or Valkyrie Profile: Covenant of the Plume because things like perspective, perma-death, damage output, and experience gaining are handled so differently. Super Robot Wars is actually pretty easy for me since, in my opinion anyway, it plays pretty similarly to Fire Emblem.

The Metal Gear series. Many games are just shoot bad guys and save the day. The Metal Gear games actually reward you for killing as few enemies as you can.

One key difference is that SaGa games tend to have a lot of controlled randomness, whereas TES has deterministic skill gains (and from Morrowind, deterministic stat gains as well).

Interestingly, SaGa 1's growth systems are not at all similar to FF2s. In FF2, your actions affect what stats you might gain (or lose), and skills increase deterministically through use. In SaGa 1, your actions during battle have no impact on your stat growth at all; in fact, the only control over esper (mutant) stat growth you have is RNG manipulation (as the game's RNG is one of the worst I've seen; it gives you the same results after a hard reset, and in combat even after a soft reset).

FF1 and FF3 aren't anything like later games in the series either, except maybe FF5. FF4 was the start of a different direction for the series and JRPGs in general.