I don't like to compare projects but Counterparty development seems to be stalled at the moment, there is no real updates or news coming out from the team and even no real business seems to be interested in using the platform, maybe with Qtum coming out the Old seems to be giving way to the new projects
One really big difference,
Counterparty has abandoned the counterparty ethereum EVM development.
I don;t know whether they will carry on with development for it.
That article is old