Well you already know the simple fact that Haruka is a game character. She wasn't anime-only like Kenji was (and heck, Orange Islands was basically anime-only), so conditions do not match.
Also, Kasumi being a gym leader was an old, known fact. Judging by sheer character, going back to Hanada City would seem normal, as well as taking over the gym. However, Takeshi staying at Uchihiko-hakase's place was clearly lead to, but you couldn't anticipate it until the debut of that particular episode. Of course you couldn't really anticipate Kenji's appearance either.
However, the end of Jouto CLEARLY was leading to the Houen region.
Ironically, both regional scenarios were "something new". Jouto's was like a continuation at a new place.
Haruka was also the first and only time you have a main-to-main character, causing the only co-star effect (ironically that shafts every main game character that is not Haruka).
Though I still find it interesting that Masato was an anime-only character (or was he in the game for like less than 5 minutes? I don't remember him at all in the game), so only that aspect makes it slightly believeable. You could speculate that you use two siblings to cover Kasumi's aspect to prevent the "Kasumi replacing" idea.
But no, you already know the roles are way different. I don't consider it a replacement. In terms of similarity with a few things, I just say that's to retain some familiar aspects. Afterall, pokemon does contain continuous familiarity for every episode it airs.
Also, Orange Islands were a relatively small adventure. We all know that AG was a freaking new season (well the US and Japan as we all know are in different season splits, but even for Japan it was literally a new season).
Despite similarities, it's largely different. Only Masato could carry the partially add-on effect, however you can counter that his age and abilities prevent him from several different developments (and that his character of being technically smart is already portrayed to the maximum effect).
The only thing I could see Masato leaving is to get his first pokemon. Otherwise, changes are less probable. (Meaning it's also totally different from Kenji's actual case of staying with Ookido-hakase)
Similiarities, yes. Reasons being the same? No. If that were true, then eventually Haruka and Masato would leave and Kasumi would come back. Doesn't that just cause another Jouto monotonous downfall effect?
Oh right, and the impact of Haruka was astronomically higher than Kenji. I have nothing against Kenji, but the "new" character popularity impact has a huge difference between these two (it's also because of the conditions and the regions).