I installed the ISIS system in a 1989 Firebird as well as in a commercial tracked vehicle application. AAW and ISIS are both fantastic companies with excellent support and business practices. If you are running a dead stock application AAW is great, but if you want to start adding in features during the build that weren't OEM or after the build ISIS is genius.
As far as programming ISIS is pretty much same day for programming changes but its likely the initial program is all you will need. The only real challenge I saw with the ISIS system was how I was going to mount it and that's where I came up with the idea for our FabBoss product. This photo is under the dash of the 89 Firebird. I packaged the ECU, ISIS Master Cell, ISIS Power Cell, ISIS InMotion, and a Vintage air all under the factory dash and even with all of that the wiring was sooo much cleaner and tidy than any factory harness would have been.