Medical staff in the real scrubs that look like flour sacks. (I swear the movie/TV producers have them tailored to fit better.)
Research labs without flasks of colored liquid.
Characters looking scruffy when they have been up all night, but not in a sexy way.
Computer systems that slightly resemble real life, instead of the Law & Order variety:
I read somewhere the cast of Scrubs has their scrubs made for them. Regular scrubs do not fit that well.
I’d like to see actors using computer keyboards in a believable way. It seems that few performers know how to touch-type, because you rarely see actors’ fingers moving in an appropriate manner when they are supposed to be entering data on a keyboard. Sometimes they look more as if they are playing “Chopsticks” on a piano.
People using computers and are not typing constantly at an apparent speed of 400 WPM, and are using a quiet keyboard. (echoing pinkfreud)
One of those stupid CSI-type shows having the bad guy clam up and demand a lawyer.
“First you stole the pumpernickel, didn’t you?”
“I want a lawyer”
“And then you dug up the family petunia, isn’t that right?”
“I want a lawyer”
“The only way out was to butcher a sheep, wasn’t it?”
“I want a lawyer”
I’d like to see some radical character change over the course of the series (nerdy preppy character in the beginning, biker gang member with tattoos and mohawk by the end, etc), or some truly unalterable life circumstance such as being in jail from seasons 3-7.
I like to see the protaganist changing several times over the course of the series to focus on a different protaganist.
I’d like to see a time travel series planned out in advance, with times revisited over the course of the series, such that each season brings new twists on what happened in certain scenes as they are revisted by the time traveller again.
I’d like to see any series or film (probably only feasible as a movie or movie trilogy) where it isn’t aired/shown until completed and involved an actor filmed over a long period of time. Extra points for a time travel story filmed over the course of an actors life featuring him interacting with his self from different time periods.
Any tv series fairly well planned out in advance.
Any piece where the moment of a cliche is clearly about to happen, and it happens some other way instead.
People turning lights on in buildings when it gets dark.
How about just a lab, anywhere, that actually looks like a LAB?! No sliding glass doors, no dramatic lighting (because you need to see what you’re doing), no highly paid doctors doing grunt work, people wiping down their counters, stuff not working…
Deep, cleansing breath.
The characters of Wesley and Cordelia evolved in radical ways like this over the course of *Buffy the Vampire Slayer * and Angel, which they both spun off to. Wesley in particular underwent the most fascinating arc of any fictional character I can think of, and mirrored your example in more ways that you’d believe.
I’d like to see someone turn on a TV and not just have the TV on the right channel and at the exact moment the news story begins. For most of us looking for a specific piece on the news, we have to change the channel from what we were watching before and either wait through several other stories first (or commercials), or we tune in too late, if not at least in the middle of the story.
Well, for a lot of that you just have to seek out Joss Whedon and J. Michael Straczynski.
I want to see weaponry that actually works and impacts like real weaponry. Grenades that are virtually flash and flameless, shotguns that don’t knock the Bad Guy halfway across the room, Bad Guys that can actually shoot as well as, if not better than, the Heroes.
Oh, and Michelle Trachtenberg’s boobs. 
If, by “Michelle Trachteberg” you meant “Scarlett Johannson”, then I agree with you wholeheartedly.
Damn you for beating me to the punch! 
For once a hero acting for what’s best instead of being a pious jerk.
Evil Guy:“Haha, Protagonist! You can’t shoot me, I’m holding this small child! You’ll never stop me now!”
Hero: bang
Evil Guy:“Erk! But…you shot me through the child…and you call yourself good?”
Hero: “Well, yeah, pretty much. What are the chances i’m going to be in this position again? Even if I do find you again, you’ll probably have killed a load of people before I do. Plus, you being evil and all, you’d probably kill him anyway.”
Arrested Development did this in Season 3. They were turning on the news to look for a particularly breaking story, but just like in real life, it didn’t come on right as they turned the TV on. A caption read “20 minutes later…” and the news story finally came on, much to everyone’s relief.
Those were staples of Babylon 5 and Firefly.
Quantum Leap did this to some extent.
I’d like to see something good happen in a parking garage.
Jewel Staite, a young Diana Rigg and a young Jan Smithers.
What character went through extensive changes in the half-season *Firefly *was on the air? And ignoring Serenity, who besides Mal was ever really given the spotlight?
Not Firefly. But Buffy and Angel saw all sorts of changes happen to just about everybody. Most of them intense and painful.