OS is criminal in that department. Beedrill, gyarados and ursaring were generally used when they needed quick foils (and I swear, about them, I can't remember a single beedrill focused episode in this whole show). The starters' final forms were treated like some sort of elite mons hard to ever find or defeat, bar Ash's charizard, mainly in Kanto. Cubone/marowak was a pokemon line with an interesting lore that I found disappointing that it wasn't explored.
In the protagonists' teams, pidgeotto/pidgeot is probably the only of Ash's regional birds that got the worst treatment possible. Primeape was so wasted that still hurts, one of the few non-starters/non-pikachu by the time that was allowed to have personality (even that for 2 episodes). Every of Brock's pokemon, bar croagunk, sudowoodo and happiny. And then, there's Misty's horsea, that was wasted as hell, even before kingdra becomes a thing (and lost a chance to be called and evolve in Johto).
Ash's Johto team was actually better developed than his Kanto team, but they were too much a "baby team", with only two evolved members and totodile being essentially useless, bar two or three important fights. Phanpy and cyndaquil evolving there instead in Kanto 2 and Sinnoh would help to not make them look so sidelined to Ash's Kanto starters in the league.
Houenn leveling up the game was very welcome, torkoal being the only truly wasted potential. It does have a design I sincerly like and I do lament Ash didn't use it much more. Even freaking glalie was an MVP in the league. Give May both squirtle and eevee was terrible in my opinion, when Ash's squirtle was a thing and eevee was kinda bland. I'd prefer Ash catching aipom only in Sinnoh, having it as a tag along mon, instead waste a slot that could be used to torkoal or a new Houenn pokemon that Ash could get.
Sinnoh is...surprisingly good with how they handled with the most part of the protagonists' teams. Torterra being nerfed, gible not evolving and ambipom being a vain beetch were the downsides.
Unova...sincerly, I do understand give Ash leavanny and palpitoad, so they had an excuse to not evolve snivy and oshawott AND give evolved options available to him. The only downside is that leavanny ended being an option much more interesting than snivy and palpitoad was a waste since oshawott was so annoyingly "in your face" that the frog became redundant (also, let's be fair, it didn't evolve because seismitoad is heinous). Scraggy was a great waste too, since it didn't look like it was getting better, mainly trusting on luck. And boldore...honestly, "hard to animate" isn't a good excuse to not evolve it, gigalith was essentially a stone metagross. Ash's Unova mons had this terrible feeling of being a bloated bunch. Iris whole team sounded contrieved and forced. Cilan's hadn't it so badly, but crustle stopped to have character the moment it evolved.
Kalos did a good job with the teams, but where Unova exaggerated with numbers, Ash's and Serena's teams lacked at least one more mon each. Ash kinda got the short stick this time. Noivern is very criticized, but it actually had a good development as noibat, despite no gyms. Some more battles had would be nice to it, same as Serena's mons. Clemont's team was actually pretty well rounded, I just wished he was shown interacting more with heliolisk.
Alola give me mixed feelings. At the same time, it gives the feel no one was actually wasted (bar poipole, magearna, snowy and maybe turtonator), but they wasn't fully developed too. The fact Ash didn't use incineroar at least in one battle after its evolution isn't worse than the fact litten/torracat barely had battles, despite have a good character. Even meltan worked a lot, despite be the rookie in the team.
The truth is, always will have someone being wasted or not reaching the full potential. I just can hope they try to do better each saga.