Another way to easily deal with Human Revolution second and third bosses is to use the combat rifle with the seeking bullets upgrade. Shoot in their general direction two or three clips and done.

You could also try Might and Magic: World of Xeen. Here is how it compares to your criteria:

Tutorial: Not present. However, the game is strictly turn-based and not that complicated; the most complex thing is probably knowing that you need to find a trainer to gain levels.

User interface: Is decent for a game that doesn't rely on mouse input. There are icons on the right side you can click with the mouse, but it is much faster to use the keyboard.

Streamlined customization: The only choices are character creation and choosing who to give the numerous permanent stat boosts in the game to. The default party works well enough; if you want to make your own, all you need is Thievery and Cleric and Sorcerer spells; any class can be a decent physical attacker (though some are better than others).

Combat difficulty: Combat is rather simplistic. Most of the time, combat is easy, though that can change on occasion. Each enemy has only one attack it can use, so if you can defend against that attack, the enemy becomes easy.

Decent quest tracking: There is, indeed, a quest log. (Bet you didn't expect *that* from a game of that era.) It even, IIRC, keeps track of the fountains you found which provide temporary stat boosts.

Advanced systems aren't really present. Spells are bought in stores, and a few are required, but I don't consider them to be an advanced feature in this game.

One suggestion if you do play this game: Before you defeat Lord Xeen and get the Clouds of Xeen ending, don't use the pyramids; they take you to the second game (the Darkside), which is balanced for higher level characters, and the rewards from the Darkside will ruin the difficulty of Clouds. Once you beat Clouds of Xeen, of course, feel free to go to the Darkside to continue your quest.

If I'm reading your list correctly, then it sounds like you want to try an RPG-lite: easy to get into, doesn't take forever to play, but still has classic RPG elements. While it doesn't have the crafting bit, for RPG-lite I heartily recommend:

Driftmoon https://www.gog.com/game/driftmoon

The newer Shadowrun games would be a good fit.

You might consider some dungeon crawls, like Legend of Grimrock.

Both have adjustable difficulty, and in the case of the Shadowrun games you can change the difficulty on the fly.

I also like Septerra Core, though it is a bit older and plays more like a console JRPG.

South Park: The Stick of Truth might be up your alley (unless you just absolutely can't stand the show). Has a tutorial, it's relatively short for an RPG, mostly easy combat that doesn't punish you for "bad builds" or whatever, no crafting, quests are easy to track.

Thank you for the continued recommendations, guys. I have decided to start things off with Jade Empire.