I'll try a few examples:
*Mallow's Shaymin: It feels weird they did so little with this guy, given its implied ties to Mallow and her mother and, you know, it was a fricking MYTHICAL POKEMON given to one of the main cast. It got one filler episode for limelight, annoyingly just enough to give it a personality and bond with Mallow to get us attached to it, and then remained a fairly inactive baby mon, even its one battle in the league being mostly offscreen. A shame since Mallow needed to boost as trainer (one with healing moves fit her perfectly) and come on, when's the next time we'll likely have a Gen 4 mythical in the main cast?
* Lana's Eevee/"Sandy": Another girl that really needed to team upgrade and when she got it, didn't do anything with it. Despite a lot of fanfare with the mini-sodes, Sandy was left as stagnant comic relief. Weird since it was the one main character Eevee given to a type specialist, so we could have seen them playing more with the customisation utilised on the species, evolving it into Vaporeon or at least learning it Bouncy Bubble.
* Nearly all of Brock's OS team: Geodude in particular was barely seen in spite of seemingly being designed to be Brock's mascot, and its replacement Vulpix didn't do much either.
* Sun and Moon's COTD Pokemon: I love SM but it was particularly bad with teasing captures, often for the girls who needed them the most. Fomantis, Dewpider and Sandshrew (who I'd have LOVED as a main cast Pokemon at last) all got episodes midway into the series which seemed ideal for captures, but did not happen. Dewpider in particular had potential since it already had a personality to contrast Lana's Popplio. I liked the sibling dynamic with all the secondaries against the signatures, and Dewpider could have been a different one, a more clingy 'baby' that hogged attention away from Popplio, which could have made for a decent 'jealous older sibling' arc to keep Lana busy until the latter evolved in Ultra Legends.