I absolutely loved this movie. It did go a bit more into metaphysical “what is reality really” type stuff but it was still good. I think the point they were trying to get across with the ISOs has to do with the theory of complex computer systems and sentience. There’s a theory that says once computing power gets sufficiently complex and powerful, sentient AIs will spontaneously develop in it. The ISOs are something like that, wild, unpredictable, and alive. Way more complex than Clu ever could be, and he saw them as imperfections to be erased. Clu was also partly corrupted, which is why he started going on his rampage to being with.
Something that disappointed me was when Flynn said to the guard program “I’m taking this vessel” and after the guard said no, I almost expected him to say “sudo I’m taking this vessel” then the guard lets him pass but nooooo I had to have that geek joke all in my head.