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There are differences between them, all right:
-Some Pokemon are exclusive to one game (you can find Spinarak in HG, but not SS and Ledyba in SS but not HG)
-Ho-oh appears in the Bell Tower pre-E4, while Lugia appears in the Whirl Islands post-E4 in SS.
-Lugia appears in the Whirl Islands pre-E4, while Ho-oh appears in the Bell Tower post-E4 in HG.
To add on to Lugia/Ho-oh: Lugia and Ho-oh each have a (IMO very well done) cutscene as you approach it. You can see Lugia's only in SS and Ho-oh's only in HG.