I have yet to watch any of Keaton's films (though I intend to check out The General in the near future), but it was always my understanding that the story about Chaplin cutting out Keaton from Limelight was just a rumor (the IMDB also says this...admittedly, the IMDB isn't the greatest source of information in the world...)
I still can't help thinking that Welles felt some personal animosity towards Chaplin (and vice versa) over Monsieur Verdoux. From what I can tell, it has never really been established just what did take place: Welles maintained that he wrote a screenplay, even outlining scenes (as I remember) in This Is Orson Welles, others have said this is false. Welles also said that the "based on an idea by Orson Welles" credit didn't appear until after the film's premiere (I've never seen anybody challenge this particular claim), which was a deliberate move by Chaplin. For what it is worth, however, David Robinson claimed that the initial contract between Welles and Chaplin stated that the film would run with the credit "based on an idea by Orson Welles". But nonetheless, since the film came out after "The Stranger" (which was Welles' only commercially-successful film in the US), and since it was a commercial (and critical) failure in the US, it isn't hard to see why Welles wanted to distance himself from it.
Given your thoughts (and the thoughts of others) on the matter of Keaton and Chaplin, as well as the (paraphrased) statement by Welles about The General, I'm even more surprised that City Lights was on his personal top-ten list (as I said before, I do think City Lights is over-rated. It is good, but it isn't *that* good). But, of course, Welles was always adept at unleashing surprises...whether pleasant or unpleasant.