In many respects TAS is the "lost" series since it's not uncommon to encounter people who never knew of its existence. It came along with a scant twenty-two episodes and then practically disappeared for the most part afterward except for die-hard fans.
I'm fine with cleaning up the original prints, but anything more than that not so much. My criticisms of TAS go beyond what's actually on the screen. Many of the stories really needed to be fleshed out more and you can't do that unless you're basically starting from scratch, and if you're starting from scratch then you should just make an entirely new show rather than remake an old one.
It is what it is even without the things we'd like to have seen. I feel much the same as I did with TOS in that I feel TOS-R went too far. We are already seeing new sequences of TOS-R being used as reference material about TOS. In a recent special called The Truth Behind Star Trek they were referencing when GR finally got the show on the air, and yet they were using TOS-R footage rather than the original footage. I found that truly misleading because that certainly isn't what viewers saw in 1966-69 and for decades of reruns.
No, clean up the prints but leave TAS alone.