After noticing that the graphics for "what new" and "wanted" on screenshots from the official website didn't match what's in the final games, I decided to nitpick the rest of the shots for visible differences. I'm including screenshots from Nintendo here as well, they seem to be even older than those provided by Smilesoft.
I'll list proto shots first, then each of my comparison screens from the final games with explanations of each change. See if you can notice what changed before you scroll down to the explanations
Let's start with the D-Mode shots from the official T2 website:
Here are my comparison shots from Speed Version:
The D-Mode icon has changed a bit. The D is drawn differently, and the landmasses have been moved around.
"what new!" has been changed to "What new" and the banner has been totally redrawn.
Additionally, each page in "What new" has its own banner text now.
"wanted" is now "Wanted!!" and has had its banner redrawn to match "What new"
What version are Smilesoft's screenshots from? The D-Shot model is exclusive to Speed, but the Denjuu in the minigame is Doon!
Moving onto some more Smilesoft screenshots detailing the D-Shot's other features:
Comparison Speed shots:
Once again, what version were they playing? The proto shot shows a Speed-exclusive phone using a Power-exclusive background.
The read text message icons have been redrawn completely. It can be assumed the unread ones were changed as well to fit the new style.
The Melo-D phone icon has been totally redrawn.
No graphical differences here, but... look at Rex's number. In the prototype shot, it matches his internal ID.
Now for the Nintendo shots: I'll just show these side-by-side with the final graphics so you can more easily compare the differences.
This one is the most subtle, and hard to see due to the proto image being scaled down. The shading/dithering of the background has changed slightly.
Color was changed from blue-grey to light brown, and the sky was redrawn. The shading and outlines look a bit more subtle overall.
The sky was changed and clouds were added, but that's not the biggest change here. Check out the UI graphics! In fact, you can compare them to those directly above. The inbattle menus don't have their own graphics yet - instead, using normal text box borders - and the HP/DP bars are completely different.
Sky was redrawn, mountains were changed from blue to grey, grass was made a much brighter green.
Here's the corresponding map from the game - notice that the cave / tree trunk colors are brown now, the tall grass sprites have been changed, as well as an extra tree added (and tree shadows):
(battle backdrops all taken from this thread)