I would say the alter egos shouldn't have their own page unless they completely give up their superhero identity. There shouldn't be a Peter Parker page. Anything there should be in Spider-Man's page since they are the same person. Jason Todd gets his own page with maybe a brief mention on the Robin page. He is simply Jason Todd now. Same with Donna Troy. She is no longer Wonder Girl. In all the issues that just have Tony Stark, Director of SHIELD, I'm still listing Iron Man in those issues.
The Flashes are a nightmare, I mean there are a bunch of issues where Bart Allen appears and he's listed as Impulse a bunch where he was Kid Flash and a bunch where he was the Flash. Now that Wally is back (sorry for the spoiler, losers) what would happen if Bart shows up in a flashback? How would he be listed?
I think we need to consider moving heroes like that into the same kind of deal we now have with the Green Lanterns, where they are listed by their real names regardless.
This would also be true for Robin and many other heroes that have had multiple civilian identities.