Avoid the SE models. They have more problems than any other kind of AmigaOne. The XE will be ok but not as reliable as the MicroA1-c as there was a problem discovered in the design of the USB ports that was corrected in the Micro.
You're better off waiting for something new, the AmigaOne series are troublesome but the people that got the working AmigaOnes don't want to sell them.
AmigaOS 4.0 will not use the onboard 68040/060 on a Blizzard so don't worry about that. The PowerVixxen LT won't include a 68k series processor on board for that reason (or so I've heard).
As for the Troika Amy '05, if/when it comes out, it will be stuck with the PowerPC 750 series from IBM which are the bottom of the totem-pole with regard to production capacity. Likewise the processor won't be as upgradable as the MicroA1-c or AmigaOne XE except the graphics card won't be on-board on the Troika and therefore you can get a good GPU instead.