see www.blackmagicmissieworks.com for the PSoC 5 based UFC-4 Universal Flight Controller and UFC-3 Open System Developers Module for custom function modules. These systems are specifically designed to support high power rocketry (HPR) flights to 100,000' and beyond (up to the FAA Class III HPR limit of 150Km). The UFC-4 will soon be available in the Developers version with all the hardware and drivers, but the developer creates their own flight control software (and hardware using 17 uncommited I/Os). Contact Tom@blackmagicmissileworks.com.
We've already contacted Tom and plan to purchase the UFC 3 with OSDM. I was hoping to find information from another group that has done a similar project so I can ask about ease of programming, control loops, and general opinion about this platform
PSoC5 is a very good choice for a flight controller. In PSoC 5 the ADC can be connected to any pin on the chip. And to scan multiple channels you have internal analog Mux implementation. There are 2 ADCs in PSoC5- SAR ADC(12 bits) and Delsig ADC(20 bits). The flight controller may have accelerometer( 3 axis), Gyroscope,Compass or may be an integrated IMU. These devices can be digital or analog. If it is analog you can the ADC to scan these sensors. If it is digital you can interface these sensors with PSoC5 using I2C or SPI and the APIs provided with PSoC further simplifies your design. And to communiacte with a GPS module you have UART as well. Talking about analog signals you can amplify them using the Programmable Gain Amplifier(PGA). You can use the filters to perform filtering as well. If you need a visual display there display routines available as component. Other than this there are large number of GPIOs which are configurable according to your need. For telemetry you can use any of the long range wireless modules available off the shelf - 434 Mhz, 2.4 Ghz.
I hope this throws some light on what you want. Let us know if you need further help.