I'm not talking about the instruction set, or teaching basic assembly (probably anything except Malbolge is suitable for that).
Let's look at just one thing every programmer has to deal with, memory.
On an LC-3, the address space is exactly 64KiB. There is no concept of missing memory, all addresses are assumed to exist, no memory detection is needed or possible, and memory mapped IO uses fixed addresses.
There are no memory management capabilities on the LC-3, no MMU, no paging, no segmentation. In turn there are no memory-related exceptions, page faults or protection faults.
When an x86 machine boots with 1MB of RAM, the 4GB address space still exists in full, but accessing certain addresses will cause bus timeouts, crashes. One must track and manage available memory. There's a BIOS, and manually probing memory locations may trash its critical structures. There's INT 0x15.
I picked memory arbitrarily but you run into the same limitations no matter what you pick. Would a students who was educated on LC-3 know how a computer keeps time? Of course not, there's no PIT, there's no CMOS clock. Would they have thought about caches? Nope.
Oh, but wouldn't a student who implements a timer emulation extension for LC-3 learn more about timers than somebody who just learned to use an x86 PIT? Alas, no. There are 20 equally easy and reasonable mathematical ways to implement a timer abstraction. A good 15 of these are physically impossible on real hardware, out of the remaining 5 two would be prohibiitively expensive due to electrical engineering reasons, one has never been implemented in real hardware due to historical accidents, and two are designs that are actually in use. So to write timer emulation that teaches you anything at all about how actual timers work, you'll have to look at and understand a real architecture anyway.
That's why educational architectures are so contraproductive. They abstract away exactly the things that make modern computers modern computers. One comes away with fundamentally wrong ideas about what computers do and how they actually work, or could work.
It's like learning to drive in GTA: in principle, there could be plenty of skills that transfer to the real thing, but in practice you'll prefer to teach how to drive to the person who didn't play GTA at all.