But J, you're talking about three (or maybe five) people in two (more or less) universes. Lora went on to something better, Alan's running the show, and Flynn is safely tucked away on Sam's SD card where he can't do any more damage.
And even while all that was going on, even though Flynn may have carved off a little piece as his personal playground, the rest of the system, which we haven't seen, has continued to evolve.
All that is visible must grow beyond itself into the realm of the invisible. Programs have lifecycles, but the system endures.
True. I realized today, as I was writing down a thought I had (I'll post it here presently) that as sad as things have ended up, and as long of a road as the surviving characters will have to travel, there still really is hope at the end of T:L, even if it's a bit bittersweet. The story is, in the end, all about redemption, which most of them find in some form or another.
Flynn: He's gone (we assume). But, he found his son again, and he found himself again, and he made things right.
Tron: He may also be gone, but he became himself again at the end. (unfortunately, as I've complained before, they made our Tron sort of impotent the whole way through, but hopefully his turn and succeeding attack on Clu at least facilitated the escape of our heroes at least a little bit, even if they could've given him much, much more*).
Sam: He lost his dad again, and he had to watch. But now he knows why his dad left and he finally knows the truth of something that has been shaping his entire life, and he has seen the Grid, and maybe somewhere a very hurt little boy can start to heal (and grow up a bit). It's going to be a big upheaval for him, yeah, but I think he's up to it.
Alan: He finally pretty much has Sam where he wants him (taking the company back), and he too may be learning the truth of what happened to Kevin Flynn soon enough...
The only two who are ambiguous in all this are Clu and Quorra. Perhaps in being reunited with Flynn, Clu finds redemption himself-- who knows. As for Q-- well, aside from seeing her first sunrise, she is entering a very difficult new life...
*If he'd just switched over and gotten out of the way, it may well have ended the same-- he was the one hot on their tail, not so much Clu, so if Tronzler had simply dropped out instead of attacking Clu, they may've just all ended up at the portal anyway if Clu didn't catch up to them in time. And Clu easily hands him his ass after his changeover, so it's not like he eliminates Clu for them. Oh well.