While it would have worked better if it had amounted to something in the long run of things, I don't think the twerps' involvement is futile just because it's episodic. You can still get new depths and challenges to give them a bit more personality even if it's not a long term thing, it's just that so much filler doesn't even try that, or only goes halfway into it before reverting back to irrelevant formula.
My issue with episodes like XYZ 20 and 21 for example is that they look like they'll be unique limelight episodes for Bonnie and Serena respectfully and give them a unique moment of being flawed. Unfortunately rather than playing it through, having their actions have consequences and them learning anything from their mistakes, we get the usual generic Team Rocket intervention that makes the first half of the plot completely irrelevant, skipping the intended climax and thus having both characters face no consequences and seemingly end the episode learning nothing. Nothing has come of benefit from this setup, not even just getting a little bit of new personality from the character in question. TR butting in is essentially a plot device to keep them flat.
Episodes like Sophocles' 'moving away fake out' for example, while episodic and basic, are at least fully realised and let us see a new glimpse of the character, we see Sophocles making an error, fearing the consequences but ultimately knowing he has to do it (if in a characteristically dithering melodramatic way). Nothing negates this character plot or dumbs it down significantly (besides maybe the others taking it ridiculously well, I get they're his friends and all, but they could have at least done a comedic faint or something) so if anything the character does get some benefit from this episode existing. Same for episodes like the Passimian episode showing Ash's more eccentric sense of altruism when a more complicated threat occurs.
This is stuff fillers should be exploited for more often, character studies, showing depths to the characters that we can't while they're progressing or busy in the main arcs. Ironically only Team Rocket themselves tended to get fully realised ones pre-SM (besides the pilot episode for Ash of course).