I'm not sure they have (managed their IPs badly). Most of those IPs were smaller, quirkier IPs that naturally became outmoded when market expectations moved up. I think Sega probably could do a better job of seeking out digital or non-traditional opportunities for their games (notably, the fact that the XBLA/PSN peak passed by without Monkey Ball or Chu Chu Rocket is kind of shocking to me) but there's no scenario where "better management" would have lead to Shinobi being a competitive full price game in 2014. Sunsetting an IP that is no longer viable is a good business decision.
In Sega's case, they haven't been able to do much to replace their sunsetted stuff, but that's OK too. They've remade themselves as a leaner company driven by catalogue sales, with fewer marquee hits.
One fundamental problem for Japanese publishers is the overall divergence of taste between Japan and ROW over the last few years. Which means if you're a Japanese publisher and you get, say, 75% of your income from Japan, it's very tough. Because Japan is a shrinking slice of the overall pie, but a) you're better at selling in Japan, b) your designers are more attuned to Japanese tastes, and c) the alternative of pursuing western tastes risks alienating the Japanese audience, which you're not prepared to do. I think this is a structural constraint that has impacted most, maybe even all Japanese publishers.
Another example of this is Square Enix wrt Final Fantasy 13. One might argue that "better management" would have led to Final Fantasy 13 being a best-of-breed world-renowned acclaim game. Instead the conventional wisdom is that the brand is tarnished, reduced to somewhat of a ho-hum thing. But the challenge is that much of what people complained about over here--the characters, the script, the dull worldbuilding, the endless linearity--may have been received differently in Japan (and we know SE feels the characters were well-received over there!). So if you're SE, you don't want to make a western-targeted product because you still make a lot of your bank in Japan, but making a Japanese-targeted product gets you increasing flak over here.
The result is a bifurcated company, where the "Eidos" ("Square Enix London" or whatever they're calling it now) side of the company makes games for western audiences (any Japanese sales are just gravy), and the "Square Enix" side makes games for Japanese audiences (with western sales being significant, but not controlling to their design decisions).
The bifurcation is even more apparent in mobile tastes. The stuff that's driving Japanese mobile success is NOT the stuff that's driving western mobile success. Another challenge for a Japanese publisher.
Sonic's brand management is also a torn-between-two-worlds problem. There's a significant audience of 8-12 year olds who want a hip, badass, quippy type Sonic. This is clearly the audience that drove the Sonic Boom reboot. Now, obviously the game is poorly made, it has problems, it's iffy. Personally I find the designs repulsive and I really hate everything I've just described. But that's a very valid audience to chase. That audience, incidentally, also drives the merchandise business which for Sonic I think is pretty significant. By contrast, there's also a significant audience of older people who remember old Sonic games and want to have classic platforming action. But products that go for one audience alienate the other, and it's not clear Sonic is viable without both. Making matters worse, the IP has been dead in Japan since the early-00s. So there's a disconnect between the development team and the global sales patterns.
Might I recommend you PM Nirolak and tell him to reply to this thread? He's very good at talking through this kind of stuff and thinking about macro-level industry threads and I doubt he'd click if no one called his attention to it.
