Actually, I do believe that is so. The other villains may be just as paper-thin as he is, but the same procedure being repeated over and over again is bad for a character and even others too like how the end TP made it like Zant didn't even matter. And like I said, it's unlikely that he's going back to his OoT or WW self. And I'm pretty sure Ganondorf's story on the CT was completed; he was arrested, banished, bright back, then killed with Ganon II on the way for FSA.
The logical reasoning behind Ganondorf returning are exactly the same reasons why Bellum, Malladus, and arguably Zant failed. They were going for new villains, something original, and it just didn't matter in the grand scheme of things. You said it yourself, why is yet another paper-thin villain needed, especially in the wake of a decade long absence? Again, we've had these "new" adversaries for so long, and what exactly do we have to show for it that has bucked the trend so much, has made those games so original, and has made them something that stands out? Pretty much nothing, as all of these revelations in recent Zelda games hasn't necessarily come from the villain at all, but rather how the game was structured from a design and gamplay point of view. Plus, you're acting like Ganondorf automatically equals some unoriginal, washed up plot. If anything, WW and TP disprove this. Ganondorf in WW was completely different from his OoT incarnation, and the game was structured in such a way that the plot was hardly an OoT rehash. TP did the same thing, with the plot twist at the ending that. Ganondorf was indeed more of his OoT self, but again, the plot of TP was completely different than that of OoT due to the entire concept of the Twili and the Twilight Realm.
I don't think that the timeline has ever served as a reason for anyone not to return, but consider this - the Child timeline has only three games on it, same as the Adult timeline. If we take a look at the Fallen timeline, we see that the resurrection of Ganon was attempted a whopping total of four times (arguably five with ALBW). So far on the Child timeline, a true resurrection (reincarnation; see edit) has happened only one time. And even then, is FSA truly the end-all game that is going to decide that Ganondorf is now obsolete as a Zelda villain? I seriously doubt it. Along with this is the fact that Demise, who very clearly is the root cause of many of the Ganon conflicts, specifically says that his curse will last through the ages, hence why he's returned on so many occasions in various forms. It's perfectly possible to have another Ganondorf plot.
Edit: Looking closer at the timeline, it would appear that FSA has it summarized as a "reincarnation". If this is true, it's logical to assume that Demise is able to reincarnate himself as Ganon as often as he chooses, further strengthening the idea that Ganondorf can indeed return with no issue.