Been over a decade since I last played both DS' EO (never played the 3DS one), bought the Switch trio to play it again. I launched both to see the status (dang, gonna miss the ability to put the card in a new DS and have my saves when I think in my Switch dying) and already I can say Etrian had random encounters whereas Moon Society you can see every enemy (icon) in first person (although a few are hidden until you get the correct ability). That alone, being able to evade random fights is a step forward. Enemies also react, if you are more powerful they run away otherwise they chase you. There are FOE but they aren't displayed on the map, they appear on the first person view with a larger symbol. The only ones that are displayed on the map are the (super) FOEs that appear only when you collect more mana than the maximum allowed in the level.
Difficulty is fine, although there are parts where you can enter sections with overpowered enemies before you should (for example, if you fall into a hole); the first battle is always stressful as you don't know if the enemies are the same ones as in the upper floor from where you dropped or if they are stronger. Bosses are fair, I think I only had to grind for the final boss (and for the second Act final boss but that was because I didn't know how to beat them). However FOEs are not, they will always be overpowered when you first meet them. I killed the FOE of the first floors when I was way deeper and advanced, although I think that's the point of FOEs, trying to stay out of their sight and just learn their route and dodge them. You can't buy weapons so you use the ones dropped by enemies or found in chests which makes sure you aren't overpowered either. And many actions to boost them use mana which is obtained while exploring so it limits the amount of boosting you can do (again, if you try to farm mana above the floor limit the super FOEs will spawn everywhere and they can't be killed until you are well into the last Act, the first time I killed one I didn't even wanted to, he spawned by surprise and caught me, blocking the escape option so I had to fight).
The battle system in Etrian is extremely simple, choose fight with weapon, with spell, defend, item or escape. Moon Society got pretty much the same options but with extra layers. The affinity between characters (aka the old evil/neutral/good, lawful/neutral/chaotic but with personalities, like arrogant, loyal, playful, etc, etc) plays a role for creating resonance between attacks (combos). Instead of five character slots your five slots are "covens" which allow for up to 3 attackers and 5 supporters (which act on their own attacking or healing the attackers) so you could theoretically have battles with 15 attackers and 25 supporters. It's kind of intimidating at first but since you start the game with 3 or 5 covens of 1 attacker only each it's as if you start with a team of 5 players and, by the time the more advanced covens appear, you have already understood most of their workings). There are more classes to choose from (24 in total) although you start with 8 and the others are introduced in the different acts.
And the story is way more mature and complex. It stretches the game a bit, though, especially because there are two sections that are basically the same (over 100 floors of random generated mazes) but with different enemies.
Seems like I didn't finish mapping the last floor of the EO, tried entering but couldn't beat some scorpions so I guess I restarted the chars and quit before grinding back to size. Looking at the cover the second one got the gunner, I remember I didn't like the idea of a gun in a fantasy setup (I bought and read around 200 books of Dragonlance but stopped inmediately when they introduced guns in the Rise of Solamnia trilogy. However Moon Society got the Gothic Gratonia who wield cannons (!) and I really didn't mind it that much.