1) All models of the E60 M5/E63 M6 were fitted with SMG III by default (US models had an additional 6MT option, however).
2) The E9X M3 would cost far less to maintain in the long run. Just to name a few things: Besides the obvious changing 8 spark plugs being cheaper than 10, which is certainly true, there are other things as well. The 6 speed transmissions are identical, but the DCT & SMG are worlds apart when it comes to reliability. Earlier DCTs were prone to software glitches but for the most part, mechanical failures are rare & more common on SMG & their hydraulic pumps. The VANOS in the S85 V10 is high pressure and is more subject to failure than the S65 VANOS, which is a low pressure system.
Also since you mention "which is easier", that also goes to the M3. For starters, the S85 is a true dry-sump, which means even an oil change is more complicated than on the S65. While certainly possible to do DIY on both, the M3 would certainly be "easier" by definition.
3) I don't own both but I've driven the E60 M5 extensively, which is the same platform as the E63 M6, albeit with 2 more doors. The choice is simple do you want a large luxury GT, or a smaller sports-saloon type of car. While the S85 V10 certainly sounds glorious and has plentiful power, the E6X platform is far from nimble. For a drive to Vegas, the M5/M6; for a lap on the track or cruising in the canyons, the M3. For daily, well that depends on what qualities matter more to you.
Good luck
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