I'm liking the active idea thread and we should strive for constructive criticism only!
I too am having mixed feelings on the naming issue. We don't want to inject needless complications. That's something I'm grappling with in hiding Anakin's transformation into Vader....
Good things I see in the suggestion are giving Anakin roots and a tangible connection to Owen. Neverar makes a good point questioning if Owen would keep the Skywalker name for Luke. Though maybe he wouldn't change it back because Luke Lars sounds silly :P Still, I don't think Owen disliked Anakin at all. He hated that he went away and became something terrible and/or died.
But if not brothers, what should the relationship be between Owen and Anakin? Do we care about Anakin's parentage? (not at all rhetorical, I'm wondering about how you all feel about it)
I agree that people don't attach significance to the name Skywalker. I don't envision Anakin as a savior of worlds.
I don't worry about Vader going to Tatooine to look up his old friend/brother Owen, or poking around there to see if that is where his son ended up. None of that has to be an issue.
Neverar, I'm not positive what you mean about when Anakin left Obi Wan? At least Obi Wan said "I was once a Jedi Knight the same as your father."