I noticed that most of the building designs changed, for the better in my opinion; I really liked the addition of an actual rocket at the Mossdeep City Space Center.
I've noticed a few things. Though at this point I've forgotten most of 'em except:
Instead of the Vigoroth helping to move/unpack Its Machoke.
Also some of the trainers had their positions moved around.
Like on the route from Mauville to Verdanturf, the Tri-Athlete is running below the Berry Patch in R/S. But in Emerald he's running in a different part.
In battles the level icon is different. There's a colon after the 'Lv' and before the level number, while in Emerald, it's just, 'Lv5' or something. And in RS, it's, 'Lv:5'