I had a 500mm for many years - wonderful lens. Optically I don't think there's much difference between the two, so choice perhaps comes down to ergonomics.
If you plan to use it handheld, over the course of a day's shooting every ounce counts which is mainly why I opted for the 500 over the 600. Though the 600 mk2 is lighter than the mk1 it is still 20% heavier than the current 500 (about .7 kg). That takes it's toll over the course of a day.
On the other hand I would certainly not consider 600 too long ... I often used my 500 with a 1.4
TC. Flight lines seem to get further and further away. Also if you already have a 100-400, an extra 100 isn't really that much different.
If you are planning to use a tripod, if you don't already have one, invest in a decent one. A lens of this size is very susceptible to wind and you need the best support you can get. You will also need some sort of gimbal head - do not even think of trying to use this on a standard tripod mount or ball head.
Optical quality is of course outstanding - the downside being it may make you unhappy with your 100-400! Of course your copy may need a little micro-adjustment to get a perfect match with your body, but I've never heard of a "bad" copy.
It will also work well with the 1.4
TC (better quality than the 100-400 at 400) - most people say it makes no visible difference.
Of course as with any super-tele, these lenses are very susceptible to atmospherics (eg. heat haze), the longer the reach, the more the effect is noticeable. The effect can be obvious (wavy cheat lines) or subtle - lack of detail. Best results need good conditions.
Cheers,
Colin
