I came from a 2005 Element EX and couldn't have been happier with the choice to go T4R.
I've never driven the Pilot so I can't give you a comparo there - I can, however, compare my experiences with the Element for 5 years and having the Trail for 1.
1) I don't agree with the "A/C Issue" mentioned earlier. The A/C in the 4Runner is about 10x better than the one in the Element. Honda A/C systems have never been their strong suit, mine would take forever to get cold whereas my 4Runner gets cold immediately.
2) Storage - yes there is a lack of storage in the 4Runner and I miss that about the element sometimes. I don't have the updated sound system in mine so I get some extra cubbies in the way back which are helpful.
3) Speaking of the sound system.... sound system in the Element was way better than the non-JBL 4Runner. So it may be worth it to upgrade to the JBL if thats important to you (but then you'll lose some storage).
4) I don't miss the 4 seat seating capacity or the suicide doors, those things were a PITA. Two MAIN reasons I am getting rid of Element and not getting another one
5) The element was a lot more comfortable on long drives; however, I wouldn't say the 4Runner is uncomfortable.
6) You'll hear people complain about the "sway" at highway speeds or the affect the wind has on it...all I have to say, is that if you've been able to handle the toaster, you'll have no problem controlling the 4Runner. I felt like there was a sail attached to my Element sometimes and the 4Runner is a piece of cake in comparison. Good to know
7) Was your element 4wd? Sorry if I missed that - but it was nice having the automatic engaging of the Element 4wd system vs the part-time 4wd in the Trails/SR5 - if you are going with a limited then it shouldn't matter. Not 4wd, an 06 EXP (first year of painted panel option)
Anyway, I'm not sure how attached you were to your element, I was a big fan of mine, but in the end it was time for the upgrade. You won't be disappointed with the switch but there will be some things you miss.
I hope this helps! Were you over on the Element Owners Club Forum? No, for me it was a work vehicle more than anything. Our fun vehicle is our Civic SI Mugen which I used to go to 8thcivic a good bit