For anything with non trivial software requirements prototype with something very much larger then you will need and then cut it down once you are close to going to production if the micro is significant to the BOM cost.
Software is always the next best thing to impossible to estimate with any accuracy, and the requirements only ever get more complex as the project progresses.
Micro choice for me is driven by several factors:
Does it have the right mix of peripherals (Including more ram and flash then I expect to use)?
Do I need an FPU for my intended woirkload?
Am I power constrained?
Package?
Development tools?
Developer familiarity?
Documentation quality?
There are no right answers here, it is all about tradeoffs, thats what makes engineering fun.
Regards, Dan.