Yeah, the Rutz idea just popped into my head the other day when I was writing something for the Profiles section. It was a strange thought at first, but it started to make sense after I pondered it for a minute. We may never know for sure why the name was changed, but I think this idea is more plausible than some I've heard.
I like the idea of separate universes, but I don't take it to the extreme like some people have done. To me, some things are just mistakes or translation differences. The only things I really consider as creating the possibility of separate universes are the time since leaving Palma thing in PSIII, Le Roof's different story in PSIV, and Lassic's differing backstory prior to PSI. Those are the biggies. IMO, the rest of the story, including Lutz, is the same even if a few names get shuffled around.
Another reason is the fact that since Noah/Lutz new of Mother Brain's existance and control over Algo, and was in hiding, it'd be reasonable to assume an alias for a number of practical reasons.
I always liked that idea. He's a smart guy, so I can't see him announcing to the world, "Hey, I'm Noah, let's go overthrow Mother Brain!"