What always really confused me about the Clones status as war slaves is that it never seems to upset Anakin, a former slave. Like, in "The Hidden Enemy" Anakin gets an expression when Slick points out he and his brothers are all slaves that seems to indicate he realizes this and that it makes him uncomfortable... and then it's never brought up again as far as I remember. Like, they really could have used the status of the clones as slaves, as well as the Jedi's complacency to the slave trade on Tatooine as reasons to his fall, but neither are ever really brought up. Also, is it ever established what happened to the clones in general after Order 66? I know they were used as the first generation of Storm Troopers but what happened after they were retired? There were thousands of them, where did they go?

oh I've thought about this so many times and it never fails to bug me. my guess is it comes from the fact that Lucas literally did not think about the implications of the Clone Army when creating them in ROTS, but it's still an issue and one that... doesn't really have an explanation. Not to mention, the Jedi as a whole were supposed to be super anti-slavery (which we know they weren't since they let prominent groups like the Hutts get away with it/were willing to compromise with said groups and also, ya know, Qui Gon literally telling an enslaved Anakin that they weren't gonna save him or his mom...), so even accepting their role in the GAR goes against what they say they stand for.

Generally, I think there were three main plausible responses to the Clone Army from the Jedi (for those who actually acknowledged that the clones were enslaved anyway):

Viewing it as a "necessary evil" and were willing to fill their role in the hierarchy. By reasoning with themselves that it was for a greater purpose, they're basically absolving themselves of guilt/responsibility. This also goes into the "well if I don't do it then someone else will" mentality where they see it as a must. -> We can also talk about the concept of "acceptable slavery" here and how we perceive Jedi who "treated the clones nicely" vs someone like Krell who saw them as expendable and sub-human

Completely distancing themselves from the source (while actively criticizing from afar, in some cases). They might acknowledge that the clones are enslaved but refuse to actually do anything about it and instead remove themselves from the war effort entirely. They see it as something that's bad, but not something they should do anything about either. If they avoid being put into roles like "General", they avoid feeling responsible. They still remain a Jedi but have completely avoided aiding the war effort in its entirety while also remaining silent about the clones themselves with the occasional sympathetic comment.

Leaving the Order. This one can kinda go with the above I guess, though I'm sure there were Jedi who saw what was going on and outright refused to be part of an institution that was actively participating in the enslavement of the clones. I'm sure there were former Jedi (and maybe even active Jedi) who helped clones desert, though we haven't seen any in canon, so I guess it's up to the fans to have that (without the white savior vibes please :|).

I think it's also important to talk about "well, who's guilty then?" because in the broad sense, the entirety of the Order is responsible, but then it varies at an individual level. Like let's look at Plo Koon who's canonly very forgiving but draws the line at slavers and actively tries to kill them on sight multiple times in the comics. I enjoy Plo Koon as a character; I like doodling him, I like reading fics with him, but he's also a High Council Member and upholds the system which keeps the clones enslaved. His character arguably contradicts itself, but because he is portrayed as nice and caring, the argument against him is "lessened"/he is not held to the same level of accountability someone like Krell is. We excuse him—and other Jedi—from the fact that he is helping to lead an army of enslaved men because he is nice.

In Anakin's case, part of me wonders if he doesn't really think of the clones as enslaved because the clones are not enslaved in the same way that Anakin was enslaved. He has a set idea of what slavery is based on his own circumstances and the way that the clones are enslaved doesn't seem to fit the bill so he doesn't really register it. Being confronted with the fact that his childhood might not be so different from what the clones are currently going through made him uncomfortable, and as such, he pushed the thought away/decided against addressing it. That's more so an in-universe explanation since I already mentioned why the story's probably set up this way but yeah. Idk how much I want to get into that, so I'll leave it at there for now.

For what happened to the clones after Order 66, they fought for the newly established Empire and continued to be produced until the Kamino Uprising (which I think was like... 16-12BBY, somewhere in between that??). Palpatine pretty quickly started integrating natborns into the Empire's military wing though the clones still made up the bulk of it for a while since the Empire needs more than one or two years to make a complete shift. Most of the clones died before they could ever retire from old age, I believe the last active clones were Vader's fist (the 501st) and the majority of that battalion was wiped out during the Battle of Hoth. Bottomline, they deserved better than what they got.

I'm 90% sure clonehub's talked about this, so I recommend checking out her blog.