I've driven both an AT and MT model at work and I find the AT models to be a bit slushy (much like most non-sport autos in general). If I could snap my fingers and make my Element whatever I'd like it, it would be a 4WD MT for sure.
Keep in mind that MT will feel quicker as it is a bit quicker since power flow from the engine to the transmission is a direct connection once the clutch is fully engaged. Autos work on fluid coupler physics so there is some powertrain loss in having an auto. Admittedly I do like the no-brainer operation of an auto, especially in winter snow or whenever I'm navigating city traffic and have to talk and/or deal with my daughter in the back seat. Just slap it in "D" and go.
The one big caveat to me with automatics is all things being equal and good, they are far more prone to drivability and performance issues as they use the fluid for not only lubrication but also power transfer and pressure operation. This opens the doors to a host of issues if proper and timely fluid change intervals are not maintained. Need proof? Simply ask any 1999-2004 Odyssey owner who has neglected the every 48,000kms ATF change recommendation from Honda :razz:.
On the other hand, manuals essentially use fluid as a lubricant only and so long as it maintains the proper friction co-efficient for the synchros and lubrication properties for the gears and bearings, you can use any proper manual transmission fluid from Honda MTF all the way down to plain old Rollback priced Wal-Mart Super Tech 5W30 engine oil and be fine. Additionally, in the event you do have an internal issue with your manual transmission, once the concern has been properly diagnosed and the part is in stock then most all Honda shops can repair the issue/component and have you back on your way the same day. No waiting for a reman'd unit to come from Honda like automatics :twisted:. This is why I'm glad I get staff pricing at work and change my ATF every 20,000kms :grin:
Honestly, the "fun" factor of a manual can't be beat and whenever I've driven a MT Element (or any MT Honda for that matter, especially the 6-speeds) at work on a road test, I just enjoy it so much more :evil: 8).