Excellent questions!
I did not want the Limited because of the leather seats (which oddly enough is probably my top complaint about my Trail Premium).
Cupholders in the 2003 (first year of the 4th Gen) had these clips that would "hold" a cup or bottle for the driver and front passenger. 2 Problems: First the clips would break down and barely hold and empty cup when off-road - let alone a bottle of water. Second they are far too close to the vertical dash panel (where there is a "bin") and too close to each other. Large or oversized cups and bottles wouldn't fit next to each other. I ended up making a wooden insert to fix the first problem, but the second was still frustrating.
Cupholders in the 2015 (second year of the 5th Gen version 2) are oversized round holders with a rubber insert that are far from each other. I can fit my 40oz Hydro Flask (vacuum insulated stainless steel water bottle) in the 2015 cupholders with the rubber insert removed, and having two of those in the cupholders in the back seat (same insert size) makes for easy grab of cold water. Is it a perfect system? No, but it is leaps and bounds better than the 2003 was.
I actually never really used those "around the corner" mirrors in my 2003 because I installed a rear-view camera in the spoiler. As a matter of fact, you don't need them in the 2015 with the wide-angle rear-view camera. You can see much more and much clearer on the dash than through those small mirrors. Although the 2015 and the 2003 were roughly the same size and "pretty much the same" frame, the 2015 does better for all around visibility with window placement and sizing. Also, I added the Rav4 heated mirrors with the blind spot convex mirrors in the corners. It was fine without them, but they are more helpful than I thought they would be.
The only two things I liked better about my 2003 were the cloth seats and the ceiling height with the sunroof option, but I am only 5'9". So, it isn't an actual problem as much as a perception. It could also be due to the roof line being so much further forward than the 4th Gen.