I've been wrestling with the 'flexibilty' of Cortex processors and I'm getting a bit hacked off with it. There are two specific issues that are causing me grief.

Firstly, you have to put in days of work on the IO pin mapping to make sure you can actually connect up the pins to the peripherals in the way you want. Vague documentation is a problem, as is the sheer size of the datasheet or user manual. I seriously doubt that all the allowed permutations are useful, but there's not so much flexibility that you can just connect stuff up and then fix it all up in the software.

Secondly, you can knobble your debug/programming port if you program up your IO configuration in certain ways. I'm staring at some boards at the moment where I can't connect to the processor and I don't know why.

If you are going to make a chip that sells on the number of features (i.e. kitchen sink marketing) then it will be cumbersome. It takes real skill and commitment to hone a design down to minimal set of functions that will do the job.