I wish the Arduino IDE actually tried to be educational instead of just being a dumbed down wrapper around avr-gcc with automatic #includes. There are so many things that could be done... stuff like showing side by side disassembly of functions, with register names displayed symbolically. Or even just basic IDE stuff, like built in contextual function documentation.

And then it should have an "export self-contained project" feature that gives you a directory containing a Makefile and all the dependencies to build your .ino, as source code form (and none of the ones you don't use), so you can easily see exactly what is getting built under the hood and can use that as a bridge to working outside the ecosystem. At the scale of 8-bit micros there's no reason not to work with copies of your dependencies, and it's very educational seeing everything in one place (and being able to hack on it) instead of having it scattered in a bunch of global package paths.

The frameworks and libraries are useful (if opaque and quirky and underdocumented), but the IDE is just so underwhelming... heck, it doesn't even manage to be a decent text editor.

Getting started with Arduino makes total sense, nobody's expecting newcomers to start off with the IC datasheet... but they should be able to eventually read the parts they need and work with it directly, instead of relying only on software abstractions. That's the beauty of these systems.