As far as the cost goes, add $750.00(cost of the MCU alone), or $1199.00(cost of a full Intellicontrol) to the price of any touchscreen, learning remote. We have done them with TSU2000's, TSU6000's and have a client who wants to use an iPronto with thier Intellicontrol. The level of flexibility and options are another plus to this appoach over a Crestron system or a Via! Valet. Add to this the price of either a "Y" cord(for video sync$1.50) or an LS1(light sensor aka last resort$100.00) or an APC2(current sensing outlet with 12volt out or contact closure$150.00) and you get the total price. We usually do the full Intellicontrol for most of our clients. A lot of people while loving automation, are not comfortable with touchscreen remotes. Having the RF remote gives the client a remote for guests or a dedicated RF zone 2 remote(works great in the Kitchen). Having the Intellicontrol remote also allows us to break the programming down for testing purposes. A typical system uses the Intellicontrol IR library and commands for source and input macros(allowing us to use the sync capabilities) and then uses IR pass thru for channel or (custom) macros.
As far as programming goes, add 1-2 hours to set up and test the MCU for source and input macros, then take off 1-2 hours for having to hunt for discretes or program "Power Pages" to eliminate point and pray macros.(you can also take off another hour for client instructions when you don't have to explain to a client why everything turns on and off automatically except the TV and VCR and why they have thier own power controls)
Troublshooting hasn't been a problem as long as you keep the programming seperate ie:power/source macros and basic functions in the Intellicontrol with the Pronto merely sending Intellicontrol commands. this is another good reason to have the Intellicontrol remote.