I like most of Timm & co's stuff, but there're a few things I wish they had done, some of which they may have wanted to do but couldn't either because they didn't have time or there was a copyright hang up (remember the Bat-Embargo against Batman's villains because of "The Batman" and the "Aquaman Embargo" because of the failed young Aquaman TV series?). I would have liked to have seen Hal Jordan menacing the League as Parallax, as the Zero Hour/Final Night stuff could have made great arcs for the show. I'm not a Hal-Is-God guy by any means but c'mon, Hal deserved better than a quick time cameo via a time warp. Seriously, where's the love? Speaking of Silver Age folk, I wish they could have somehow gotten Barry Allen in there beyond a vague reference in the form Wally saying he was expecting his uncle over for the episode with his Flash museum. And on the subject of Wally, I lament that they never showed Wally interacting with Kyle Rayner, or Nightwing/Dick Grayson for that matter. I also thought it was a waste the way they reduced the Martian Manhunter's role during the Justice League Unlimited era, given that the big green guy was cooler than most of the heroes who came in through the revolving door, including Green Arrow. Yeah, I said it, the Martian Manhunter IS cooler than Green Arrow.
It was also a shame they couldn't get the JSA in there, but again, that was probably more of a copyright issue than for a lack of trying, hence the Justice Guild, homage and parody of the JSA as well as the old multiverse concept. (I'd throw a tantrum about not seeing Alan Scott or Jay Garrick as individual characters, but they tie into the JSA debacle)
But all that aside - and the fact that reducing Aquaman to a guest star on Justice League before the embargo was just plain wrong - I enjoy the bulk of what was given to us by these guys.