Lisanna should have never being brought back. She's little more than a plot device to motivate Mira/Elfman in fights, which is exactly what she did when she was "dead". Other than that the only thing she has caused are stupid ship wars which are also pointless since it's clear NaLu will be Natsu's endgame ship. Even more, with Mira and Elfman being irrelevant both in the current plot and powerscale, she adds literally nothing to the series at this point.
Makarov should have died either in Tenrou against Acnologia or in Alvarez when pulling that last Fairy Law against the Alvarez Berserkers. Tenrou situation can be excusable, but him being revived at the last second clearly showed Mashima at that point didn't give a flying f*ck.
As much as I like Gajeel, he should have died when Bloodman took him to the afterlife. Universe One was casted after Bloodman did the deal, so Gajeel's return was another proof Mashima wasn't trying.
Freed and/Bickslow should have been killed off at the start of Tartatos arc when Tempesta poisoned them with the Magical Barrier Particles. I do like them, I do really do, but they're only marginally better than Lisanna post-Tenrou and nowadays their only function is being Laxus simps. Their efficience in battles during the current arcs was made clear when Gray alone easily defeated them without trying, proving they're useless against any Spriggan-tier or above enemy. I would include Evergreen, but she has the ship card with Elfman, so killing her is more difficult. In the same vein, Yajima should have also died there.
Happy surviving Jackal's suicide explosion (able to detonate an entire city) was complete and utter bullcrap.
Minerva shouldn't have been redeened and should have been killed in Tartaros, maybe killing herself when Erza would try to appeal to the good side still remaining in her, spitting in her face and announcing once more her hatred against her and Fairy Tail in her dying breath, showing not all people have the heart to be redeemed and get a second chance (Mashima with Edens Zero mentality would have pull that tho).
Some of the minor Fairy Tail members + some members from the other guilds should have died both during Future Rogue's rampage in Crocus and Alvarez arc. You're telling me that there is a country scale war and only the bad guys effectively die? The Future Rogue case has a justification with Ultear casting Last Ages (though that all the people who were killed died in that exact minute is eyebrow rising at the very least) but Alvarez has no justification. I'm not saying Mashima should have gone full Akame ga Kill mode and killing everyone, but characters no one cares such as Macao, Wakaba, Droy, Nab, Laki, Eve, Beth, Risley, Rufus, Orga, Sawyer, someone from Quatro Puppy, etc. should have been good enough to get rid off, as they're little more than wasted ink. That way the war against Alvarez would have actually show some stakes and would have at least gave some redemption to Alvarez as an antagonistic force.
Lastly, I'm not saying they should have died there, but if Wendy and Carla would have died when they activated Face's self-destruction spell it would have been one of the best deaths from the series.