If I remember correctly the DSi XL measures 10.7 cm on both screens (4.2 in.), whereas the 3DS's current design has a top screen measuring just under 10 cm (3.53 in.), and a bottom screen measuring around 7.7 cm (3.02 in.).
Personally, I think that's one of the quirks that I haven't been too happy with. The screens having two different sizes aesthetically looks a bit awkward to me, and it also might be a bit of a bummer in concern to practical usage, as developers have always found clever ways to use both screens simultaneously on the past DS's, such as cutscenes that cover both screens continuously. I mean, it's still pretty minor I think; the difference is fairly negligible, but whatever the case may be I'm sure developers will be able to work around it, maybe even use it advantageously.
Also, concerning the screens, I'm not too fond with the bottom screen lacking 3D (Nintendo seems to be neglecting this screen a lot, haha

). I can understand where Iwata was coming from when he discussed how fingerprints and other smudges would damage the 3D effect, but it still would have been a viable option to have for those using a stylus or just buttons -- of course whether or not you'd want to use it would depend on the specific game. Maybe production cost was a contributing factor in removing it, or the 3D effect might become too overwhelming with both screens active, but it would be nice to be able to diversify your settings, where you could play around with how much of the effect you want on both screens.
And it seems a lot of people are expressing their dissatisfaction with the arrangement of some buttons, which is concerning me a bit, too. Unless this "slide pad" dominates the majority of gameplay functionality, people wanting to use the D-pad could have a hard time of adapting to that downward placement, as the D-Pad being level with the A and B buttons has usually been a given since the Game Boy's early days. I like the concept for the Start, Select, and Home buttons too, but I'm kinda fearing that they'll turn out to be cheapy plastic bumps rather than conventional buttons, where they might not respond on the first push (a similar to scenario to some of the past DS line's "mushy" buttons). Of course, I can't make that generalization without using it first, so we'll just have to wait and see...
And just a quick question, but is the microphone on the 3DS located right under the start button? I'm looking at a picture of one now, and there's this seemingly arbitrary dot right at the end of the bottom screen.
And also, remember too, that the 3DS model shown at E3 was just a "prototype," so it's very likely Nintendo's listening to fan/consumer(
/especially shareholder) feedback. I'm afraid it's gonna be a long wait 'till we get the final presentation though...