These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Crowning Moment of Heartwarming: Bugs spends just about the entire movie being nicer to Daffy than he usually is in the cartoons (well, maybe not the entire movie) and was the only one who knew right from the start that firing him was a bad idea. He looked like he genuinely felt sorry for him after the main page quote.
Ron Perlman as a wimpy Acme exec is about as far from Clay Morrow as you could possibly imagine.
Ho Yay: Whether or not Bugs is really that depressed without Daffy, he certainly goes to pretty great lengths to get him back. His less-than-family-friendly humor is also lampshaded by the female executive:
Kate Houghton: Okay, about the crossdressing thing: then, funny; now, disturbing.
Bugs Bunny: Lady, if you don't find a rabbit wearin' lipstick amusing, then we ain't got nothin' to say to each other.
Just Here For The Looney Tunes: One of the biggest complaints about the film is how the human characters for "hijack" it from the Looney Tunes character to the point that the latter can easily be removed without burdening the plot. That said, the parts where the 'toons are on screen are considered the best.
They Wasted a Perfectly Good Plot: Surprisingly little is done with the Blue Monkey's magical power of turning people into monkeys. At least in the finished film. The DVD special features give us an alternate climax where the Blue Monkey's powers are used to create some truly wild and over-the-top situations.
Daffy crashes the Batmobile into the studio water tower, causing it to topple down... and somehow, Yakko, Wakko and Dot don't come spilling out of it. Sadly, Warner Bros. has a knack for pretending they never existed.
Considering the Executive Meddling and all the cut scenes from original drafts, this can be said for quite a bit of the film unfortunately.
Nightmare Fuel: Scooby Doo viciously bearing his fangs and growling at Matthew Lillard can be a bit discerning due to being out of character.
Tear Jerker: Daffy ranting to Bugs about how he's always second rate compared to him. After a humorous degree of self slapstick and Daffy having his tail on fire, he just says "What am I talking to you for? All you have to do is munch on a carrot and people love you." Followed by Bugs looking like he's genuinely saddened by Daffy's words.
Unpopular Popular Character: Daffy. An underlying theme of the movie can be said to be of his designated Butt Monkey status and unappreciated role in comparison to Bugs Bunny. The movie outright lampshades the fact that despite his unpopularity, he is out and out pivotal to the show, and Kate even frustratedly points out how no one and yet everyone can love him at the same time. This is what leads to the page quote about how while Daffy has to endure pain to get laughs, Bugs just has to 'munch on a carrot' to be effortlessly lovable.