MS really could have owned that market. ActiveSync made sure they didn't. They were a good 3-4 years ahead of everyone else tech wise. However, their dev stack was awful and full of gotchas. Apple and Google imploded that and made it easy to dev for. Their crazy BOM build system was a fork of visual studio 6 which was cobbled together with CMD scripts. Then on top of that the OS arch was different than pretty much anything else. There were some seriously bad spots where if you used the wrong system dll you could crash the box. Oh you need a new firmware to fix that good luck as there is no built in firmware update on your box. Have fun spending 2 months getting that patched firmware out of the company too.
Your guess about different depts is almost right. They also outsourced portions of it. Some parts were internal. The licencing around it was byzantine. Also portability was shoddy. That was due to the MIPS/ARM ISA environment. Every phone was slightly different from each other (you can see similar issues today with ARM dev boards). x86 did not end up there as IBM compat was king and if you didnt have that no one bought your board, ARM/MIPS do not have that type of market force. You had to in some cases ship an executable for each phone. Then on top of that the phone carriers wanted to charge 40-50 dollars per megabyte sent/recv.