Working in C means you get restricted to only doing things which C can do, and you're out of luck if you want to do things that C can't do: unaligned accesses, tail calls, saturating arithmetic, overflow detection, exceptions, stuff like that. IR allows you to do all this, at the expense of being considerably more complex and painful to use.
Of course, if your compiler don't want to do any of this, then C is a perfectly valid choice, as it doesn't tie you to the LLVM toolchain --- see Nim, for example. But as soon as you venture outside C's comfort zone, working in IR starts paying off.