An even shorter way to say this is that stack-based VMs are more high-level. With a register-based VM, you shift some important questions (like register allocation, and handling temporaries) to the compilers. With a stack-based VM, the compiler can be simpler, but the JIT will need to be correspondingly more complicated.

Which one to choose depends on how it is all used. For .NET, multi-language targeting was seen as an important design goal, and so making the bytecode easier to target was prioritized, with all the complexity relegated to JIT.

Long-term, I think it was a right solution in general, because most platforms seem to be moving from JIT to AOT; and with AOT, having the complexity in the bytecode-to-native compiler still has the upside of DRY, and slower compile times stop being a downside.