Beast Wars actually continued in Japan except it changed animation styles (to more traditional anime style) and actually DID go back to Cybertron.
The difference with Machines is since Fox purchased the series (not the franchise or brand mind you) they felt they could micro manage far too much.
I'm sure you'll agree that Fox in the 90s was a terrible, terrible entity that felt they had to micro manage everything (usually horribly). Heck, we still see glimpses of that today. Although I liked the Saban shows on Fox and I LOVED FoxKids on Saturday mornings, there are more then enough reasons I was happy to see Fox get out of the Saturday Morning Cartoon circuit.