I have "combined" sites before, because two tech topics I'd been writing about kind of converged as new technologies arose, and it didn't make as much sense to maintain both sites. So I actually redirected BOTH to a whole new site and gave it a nice big marketing push for readers. I set up my 301s page by page, so Google would see "Hmm, this is the same page at a new web address." It was pretty smooth and seamless - I think the algo is fine with moving content, it's just sometimes webmasters don't take the right steps to communicate this so a machine can understand. Which is why the feature in WMT where you can tell Google you're moving the domain to a new one is nice - added insurance that they'll understand what you're doing.
You may see a slight drop in traffic for a bit, but I wouldn't expect too much grief as long as your 301s aren't just homepage to homepage.