So I'm playing Betrayal at Krondor and despite the omission of a couple of features (like a quest tracker and tutorial), the game is structured like any number of RPG's that we play in 2015.

Some Examples:

Things like story progression taking place through custcenes and side quests giving an expanded view of the charactes are something we see a lot of now. (Mass Effect)

Leveling is done by using that skill. So the more you use magic the better you get at that. (Skyrim) (

Overworld fast travel though temples after discovering a new one. (most open world games)

I find this to be fairly advanced, especially for 1993.

So what are some older games that looking back are actually quite modern in function?

Planet's Edge is another one from that time zone.

There are a few games with New Game+ features that predate Chrono Trigger. Here is a partial list:

Zelda 2
Dragon Wars (no need to beat the game here)
Wasteland (original release came with a program to do this, but later releases lack it; haven't checked the GOG version)

Also,
Magic of Scheherezade (NES) has combo attacks
Saga 2 (Geme Boy) has a Memo feature that stores conversations you've had
The Legend of Zelda (NES) has an auto-map for dungeons (check the pause screen)

If you consider leveling up skills by use as a "modern" feature (I don't), I can add a few other games to the list
Final Fantasy 2 (Famicom)
Dungeon Master
Wasteland (but not its sequel, for whatever reason)

To me the old LucasArts adventures, especially the first two Monkey Island games, were better designed than many adventures that came after them till this day. They had three features that made them very advanced in user-friendliness for the time: You could not die through missteps, you could not get yourself into an unwinnable situation by missing items early in the game and then being cut off from access to them when you needed them much later, and you were always working on several puzzles at the same time, more like the questing that makes RPGs fun than the very strict linearity of "find out what I want you to do next or get hopelessly stuck" that makes quite a lot of other, even more recent point and click adventures so frustrating.

Warlords Battlecry.
- The persistent hero system.
- The ironman permadeath system.
This is why I can't stop playing the game.

Permadeath isn't what I would call a modern feature. I note that both Rogue and Wizardry had permadeath. (In the case of Wizardry, I actually consider it a misfeature.)

A modern hipster feature, then. There are plenty of games with it, it's just not really mainstream.