Interesting question, since HomeSeer has been discussed a couple times recently on the ECS mailing list. I was an ECS (DOS version) user for 8 years. The product was very stable, but then the developer (Mark Gilmore) had to abandon the project while he pursued other career options. At that point, I made the decision to switch to HomeSeer and have been happily using it for about 2 years. I did run both systems in parallel for a while as I migrated functions.
Mark Gilmore has reformed his company and is actively developing and supporting ECS again. I haven't done much with the new ECS Windows versions, so I cannot really compare the two products from a user or web interface perspective. I can state that the "rules engine" in ECS DOS was EXTREMELY powerful, but the product was built before Windows and the Internet became prevalent.
So, ECS (in various versions) has a good, long, track history. But the ECS active, online, user community is MUCH smaller than the HomeSeer active, online, user community. There is a lot to be gained from a community that shares ideas.
What will the future hold? That is hard to say, both are small companies, but HomeSeer has seen significant sales growth in a shorter time period. HomeSeer Tech seems to be aiming at a more professional installer market recently and their price increases make it closer to ECS's price, so HomeSeer is not the economical "take a chance" option that it used to be.
Am I happy with HomeSeer now? Yes, mostly, but nothing is perfect. Do I regret the switch? No, but it took some work. Do I wish I had stayed with ECS? Maybe, now that ECS is active & growing again. But I don't live my life in the rear view mirror and second guess myself. Would I switch back to ECS? No, mostly due to time and cost of doing so, unless HomeSeer becomes a dead product (and I don't see that happening).