I (conceptually) agree! But there's different sorts of compilers, and they have different requirements, which (should) materialize in the code representation. An offline C/C++ compiler has different requirements than a JIT JavaScript compiler, and so their architecture is very different. The IR should be express the relevant operations/data structures well and should easily support the analyses/transformations. If LLVM is a good fit for you, that's great. But in many cases, it's not.
I've been bitten from being warned about not writing my own IR (effort concerns), and in hindsight, it would've been the much easier way, both for low-level and high-level transformations. IMHO, people should not be afraid to roll their own IR and make it a good fit for their use case.
> one could at least use MLIR
MLIR is a nice idea (and great for selling/publishing). I find the implementation to be somewhat lacking and constraining, difficult to work with, and not particularly efficient.
> no one wants to learn your custom IR
That's a problem, but there's no silver bullet.