Hi, I am new here, but have spent 30+ years designing hardware.
1.. ATxmega engineering samples are available to qualified users. So far it seems the only ones they have are ATxmega128A1, I have two due here today or tomorrow.
2.. Providing 5V I/O capability isn't even common on FPGA's! Some have 5V tolerant inputs, but not all. Most have maximum 3.3V on the IO cells. For example the very inexpensive and popular Altera Cyclone-II uses 1.2V for the core and in my case I use 3.3V on the IO. You can drive 74HCT (or equivalent type) logic from the 3.3V outputs. This is because the TTL threshold is within the range of the 3.3V outputs. In adapting some older designs to use FPGA's instead of processors I have connected directly to things like 75HCT573, 74HCT574, 74HCT138 devices.
Because most of my work involves EMI/EMC certification and we have proven designs based on 5V parts - such as MAX232's and the like we want to make as few changes as possible to reduce the risk. So in many instances I use SN74LVCC3245 dual voltage translators to go between 3.3V and 5V subsystems. Unfortunately they are not available in DIP packages (at all) but if an Arduino design was done with a 3.3V core then something like this could easily be hand soldered anyway.
3.. Look at something like the Diecimila board - it uses the FT232RL which uses a 3.3V logic core. Although you can choose to run the IO section at 5V if you need to.
4.. 5V logic became common when structures within the IC's were pretty large. As technology has improved and geometries have shrunk, the chips CANNOT be made to work on the higher voltages. If you want the low power and the performance advantages, then just suck it up, you will have to use translators.
The geek!