I mentioned all this in the Innoventions thread, but I'll post it again...
My main principle is that Tomorrowland should actually fit its original theme of Science Fiction and science fact...A healthy mix of fictionalized adventure and the excitement of discovery, a high-tech, futuristic parallel to Fantasyland with it's basis in the real world and Disney's own franchises. It should absolutely not be what it has become, which is a vague kind of Universal Studios-style dumping ground for what franchises Disney has bought or licenced.
So, that said, I would keep Space Mountain, the Astro-Orbitor and Star Tours (under duress... In my ideal world, it would be a Star Trek ride instead of a Star Wars ride, since Star Trek actually fits ideals of scientific discovery and optimistic futurism). I would keep Autopia but refurbish the vehicles into clean alternative fuel models. I would also keep the Submarine Voyage but get rid of Finding Nemo, retheming it to Disneynature. All of those screens and projectors would be utilized to show actual footage of wildlife and ocean ecosystems.
While we're at it, I would keep Astro-Blasters but retheme it to Stitch. Basically, you are an agent of the Galactic Order charged with hunting down and "stunning" Dr. Jumba's experiments, in particular Experiment 626. Then about half-way through you meet up with Stitch, switch allegiance and help him fight off Captain Gantu and the Order.
Innoventions is out, and in its place is a permanent Tron attraction. You would enter through the turntable, and the old Tom Morrow introduction part would become a "enter the grid" moment where you're "blasted" by the digitization laser (aka: normal lighting would be in place until there is a flash of light, after which a grid light effect would be projected onto the crowd, which would blink out square by square. When the entire room is dark, the UV lights would come on and you can enter the attraction). Inside on the first floor would be two or three banks of original-style Lightcycle games like those old motocross arcade games, but with 3D screens on the interior, each bank linked together into a single race. There would also be Disk Wars games utilizing motion-tracking Kinnect-style OS. On the second floor would be Flynn's Arcade and an End of Line Club cafe. It would also have other features like interactive floors, probably a souvenir stand, and such.
Oh yes, and I would bring the Peoplemover back. When it hits the new Tron attraction, it would basically slip into the Tron Tunnel. Tronage would be projected on the walls, UV lights would come on and fibre-optic piping would activate on the Peoplemovers, making them look like they're in the Grid.
For an e-ticket, I would realize a plan that was proposed for the remake of Tomorrowland in 1998 but never went ahead. Basically it would involve gutting the basement of Space Mountain, including the theatre, and install a version of Dinosaur that blended with the Primeval World diorama. This Primeval World attraction would be visible from the train, with the gimmick that the time warp from the Dino Institute has bled over and brought the train into the past. The foyer would have some dinosaur skeletons and actual fossils on display. Speaking of displays, I would return the NASA attraction to the space now occupied by the Star Tours' Fastpass machines. Somewhere, perhaps along the Peoplemover, in Star Traders or Red Rockett's Pizza Port I would have a display of Disney Sci-Fi film props (i.e.: from Rocketeer, 20,000 Leagues, Black Hole, John Carter, etc.)
I would reopen Starcade as a DisneyQuest. Also for entertainment, I would bring in actual SoCal DJ's to spin electronica, dubstep, house and other comparable styles of music in the evenings, basically turning Tomorrowland (or at least the space around Tomorrowland Terrace) into a nightly weekend rave. I'd want lots of sound, lots of light, lots of activity... make Tomorrowland the place to be after dark...
Anyways, those are my thoughts. But I am not an Imagineer, so they're not worth much. Whatev's.