Sounds like a good reason to write modular code in 'C'! I have converted a lot of my old 8051 code across to AVR to get the performance boost as well as cheap micro's with eeprom & a/d on board. The 'c' compiler isolates most of the architecture from you.
I'm currently converting an app written in 'c' for the AVR back to a 8051 core device - the SFR stuff has to change, but the core structure of the code is identical. If you need to write assembler - again, keep it modular.
All said and done, most micros all do the same thing and have similar peripherals - choose the one that best suits the application