I've been configuring a toolchain for Algoram's programmable radio transceiver, which has a SmartFusion 2 containing a Cortex M3. Until today, I've been working with GCC 5.1. Building GCC for cross-compilation on a no-MMU, no-FP processor and a software platform that doesn't support shared libraries isn't trivial, though it should be. GCC has many configure scripts, one for each library that it builds and at least one for the compiler. You run across many configure issues which are difficult to debug. For example, the configure file, a macro-expanded shell script, doesn't have source code line numbers from its configure.ac file. Error messages do not in general indicate the actual problem, and are difficult to trace. Figuring out what to fix is far from trivial. I ended up not being able to use multilibs (which would have allowed me to build for FP processors like Cortex M4F as well), couldn't link in ISL, couldn't build libjava.
Some of these are beginner problems - I'm new to building cross-toolchains and have avoided autotools as much as possible before this project. But not all of them.
One would think that we could build a better system today than such voluminous M4 and shell. Perhaps basing it on a test framework might be the right approach.