I'm not worried at all about Bad Machinery not living up to Scary Go Round because I remember when John Allison pulled this same stunt before. Bobbins started out as a office-romance kind of comic but eventually went into more fantasy/adventure territory, at which point Allison decided to end Bobbins and start a spin-off focused on that comic's secondary characters, Rachel and Tessa. Within a year or so, Rachel and Tessa were minor players in this new comic, Scary Go Round, and the core cast was almost entirely the same as the primary Bobbins cast: Tim, Shelly, Amy, Fallon, Ryan, etc. And then SGR evolved on its own, quite naturally, to be better than Bobbins had been before.
I'm fully expecting to see the same thing happening with Bad Machinery. I can't imagine that Allison will be able to stop writing stories that feature the SGR cast any more than he could stop from featuring Bobbins cast members in SGR.