First off, the Grogar plot twist was a stupid idea. The writers could have had Discord bring back the villains in a way that didn’t involve bringing back Grogar, hyping him up to be the big bad, then throwing it all away with a stupid plot twist. They wasted so much potential because they wanted Chrysalis, Tirek, and Cozy Glow to be the villains instead of some new guy (new to G4 at least).
The biggest problem about all this is that it made Discord look like a complete idiot and the three villains look much smarter and more competent than they actually were. It’s true that this was by far the biggest and most competent threat Twilight and her friends had ever faced, and the only reason Twilight won was because the student six and two ponies were somehow able to unite everycreature after they all turned on eachother (not to mention they somehow succeeded in turning the CMCs against each other despite being friends for so long, and Lyra and Bon Bon who had just got married), all of Equestria shows up to save Twilight and her friends just as they were about to die, and they wouldn’t have even gotten that far if Discord hadn’t gotten lucky and freed Starlight Glimmer. None of this makes up for the fact that the only reason the villains got so far was because Discord gave them all that power. Discord could have monitored the villains when they retrieved Grogar’s bell and stop them as soon as they thought to betray him, but he didn’t. He could have easily stopped the three villains from using the bell against him but he just stood there and did nothing. He could have just decided not to bring them back and instead send Chrysalis to Tartarus. Discord could have stopped the villains at any time but instead he just let them betray him.
What the writers should have done is have Chrysalis be the one to break Tirek and Cozy Glow out of Tartarus and then the three of them work to find information on how to increase their own power, learn about Grogar’s bell, and retrieve the bell without Discord’s involvement. That way they’d still be the main antagonists of season 9 but they would have been independent from Discord (whose character wouldn’t have been ruined) and there wouldn’t have been as much wasted potential since Grogar wouldn’t appear at all (and his bell might not have even been referred to as his bell, or it could have been a different magic absorption artifact).
I still dislike The Ending of the End for the plot twist, but without that plot twist, it would have been a good finale.
As for the villains being turned to stone, I don’t feel bad for them. Chrysalis and Cozy Glow both had multiple chances at redemption yet they rejected friendship every time, not to mention Chrysalis was part of the reason Cozy Glow and Tirek didn’t reform. Not enough is known about Cozy Glow’s past for her to be sympathetic (it’s possible Cozy Glow killed her own parents offscreen which could be why we never heard anything about them, in which case, nobody would have felt bad for her anymore). I think if any of the three villains should have been given a second chance, it’s Lord Tirek, but even he’s too far beyond redemption at this point.
But I don’t think Discord should have been allowed to choose their punishment. I think Twilight should have been the one to choose their punishment, and she should have given each of them one last chance at redemption, which all three of them would refuse.
I think the villains in MLP were too easily forgiven (except Sunset Shimmer), especially Starlight Glimmer who was arguably just as bad as Chrysalis, Tirek, and Cozy Glow yet received no punishment for her actions and everypony forgave her just because she had a tragic backstory (which was nothing compared to Tempest Shadow or the comic version of King Sombra).