x86 doesn't have thousands. That's overstating it by quite a bit. The assembler I wrote contains 1095 encodings. It's from ~2004 but 100% complete at the time, so sure new instructions have been added since. But those are encodings. SAL has like 8 encodings, SAR has 12, CMP has 14, etc. These encodings are just different ways to use the same opcode but with different source/target parameters (8/16/32-bit immediates or registers, etc.)

Someone wrote a script that disassembled all the binaries on their Linux machine and counted the number of actual instructions used (mostly by gcc, of course). Only a tiny fraction of the total instructions were used:

http://0x80.pl/notesen/2014-01-01-instruction-utilization.ht...

Just take the top 30 of that chart and learn those. The x86 contains a lot of instructions that no one needs to worry about. Things related to the ancient segment mode or x87 floating point, OS-privileged instructions (context switching, HLT/LIDT/etc.), AMD-only 3DNow, etc.

The ISA is not the hard part anyway. Dealing with the ABI (System V on Linux) to interface with C/C++ code, the kernel syscall interface, position independent code/executable (PIC/PIE) are somewhat bigger concerns and are going to apply to RISC as well.