I made the same switch from Indigo to ISY-994i this week. Like you, I loved their product but I just couldn't justify buying a Mac Mini to run it.
I have about 20-25 devices and I unplugged my Indigo PLM then added devices using a combination of 'Remove Existing Links' and 'Add devices found in links and keep existing links'. Everything worked pretty well. I had one switch that didn't play nice. I think due to some communication issues. The battery powered TriggerLinc and Motion Detectors were a pain as usual, but all is well now.
Thanks for the reference to Roomie Remote, I read your post about 5 hours ago and have since bought it and have it running my entire living room. Nice product, a little buggy but not too bad.