I went for Mystogan, Meredy and the GOI + WS.
For Mystogan it's because I feel he was rushed out of the series too quickly. Laxus considered him as the biggest threat in the FF arc and he showed some badass magic despite how short Laxus vs Mystogan was. Had he been kept around it could have led to more Wendy/Mystogan development and the dynamic of having two Jellal's wandering about. On top of this, it would show that Holder Mages can be top tier, though admittedly I'm not sure how Hiro could explain Mystogan's staves becoming more powerful. A good example of Mystogan's wasted potential was the August fight, had Mystogan been around we could have seen Mystogan and Gildarts vs August rather than Cana and Gildarts vs August (this is just my opinion, but Cana shouldn't have been there at all, the family drama was just unnecessary).
I picked Meredy because of her magic + relationships with the rest of CS and Juvia. Maguilty Sense has incredible potential in two different ways: use among allies and use against enemies. Her ability to link an ally to herself is pretty insane even conceptually, it's like a Union Raid but without the needed bonds, however the real potential is with her ability to link two other allies and herself together. The sheer idea of her linking two people like Jellal and Laxus to herself is pretty epic, mainly because those two are beasts singularly, but if you linked them together and merged their Magic Power + Meredy's? That would be something to see. As for her potential against enemies, she'd be a great support mage. Is an enemy too mobile? She can link and damage herself to hurt them. Is an enemy intangible (akin to Juvia)? Maguilty Sodom and Maguilty Rays can help there. On top of her magic not being used to its full potential, I don't think Mashima has given her any real meaningful scene since Tartaros, and even then that was her crying about Ultear. Why not explore her relationship with Juvia or the other members of CS? We know that Juvia and her are great friends, but we only ever get glimpses of it since Jellal's interaction with other FT characters usually take priority. There's also her relationship with the newest members of CS, we know that Jellal and her have a stable and trusting relationship (akin to father/daughter or big brother/little sister) but I can't ever recall seeing her having an actual conversation with any of the OS after the timeskip.
As for the Wizard Saints and the Gods of Ishgar... so much hype was wasted. Wizard Saints in general were pretty hype, because while it doesn't necessarily mean they're THE strongest 10 wizards in Ishgar, they still have to be pretty damn strong to obtain the title, as well having the right attitude and amount of knowledge. Whilst Wizard Saints 10-6 were kind of dehyped in GMG due to Jura being the number 5, that was no sleight against them... until Laxus beat Jura in GMG with just three months of training. Yes, it was an extreme-diff fight, but that doesn't change the fact that a Wizard Saint who trained for seven years got beat by a character who only trained for three months. I don't even care what training Laxus was doing, I just feel bad for Jura and the other Saints. This being said, I could swallow that happening because of how Ooba hyped up the Gods of Ishgar: essentially, they're absolute monsters that no one can touch or even come close to. To make the hype even sweeter, we then got to see Warrod in the Sun Village arc, a guy who afforests deserts for fun and can spawn a 2000 K tree pretty casually. This indirectly hypes the other Gods of Ishgar, they're all above Warrod, and Warrod alone is pretty hype. Then the timeskip happens and we're introduced to Wolfheim and Hyberion, the former being shown as a take-over mage, the latter looking like a vampire. They reveal that God Serena defected to Alvarez, so at this point it seems like Hiro is trying to foreshadow a Gods of Ishgar vs God Serena match. This does actually happen, but they're worfed, used to simply hype God Serena, with them getting wrecked by base God Serena, and then getting annihilated by him when he goes all out. Now to be fair, Hyberion does get a complement from August for his Vampire magic, but the fight was just underwhelming. Not only was the majority of it off-paneled, but the second the GOI start to fight back they just get squashed. And to make it worse, God Serena himself is then worfed to hype Acnologia, meaning that we'll likely never know how powerful they actually are. These guys got screwed over hard, especially since Fairy Tail members have stomped Spriggans who are supposedly on/near God Serena's level. Overall, their placement of power made no sense, not to mention that all of the hype we had since GMG was wasted just to hype a villain who was just used to hype Acno. They could have been so much more, but apparently one year of training not only surpasses Jura's seven years of training, it surpasses it so much that whilst Jura would likely lose to a single God of Ishgar, a Fairy Tail top tier would stomp Jura, Warrod, Wolfheim and Hyberion with ease. I'll never understand why Hiro wasted these guys.