The smart key (I didn't think I would appreciate it as much as I do now), the 20 inch wheels, the optitron gauges are really cool, i personally like the brilliant simplicity of Toyota's infotainment system, the XREAS is awesome (clearly noticeable if you drive the two side by side), having full time 4 wheel drive is great as well and makes for a more luxurious feeling day to day ride. Everything is better IMO and I wouldn't have a T4R if it was an SR5.
I traded my 2012 limited because I hated all those features!! Expect the smart key that was cool. 20" wheel look weird to skinny IMO, XREAS made the Runner feel heavy as hell and it showed on my mpg getting only 15.9 on city. Now my new 2012 4x4 sr5 is getting 21.0 all city and love the way it drives. That's just me but get what you want that's what counts. Good luck