Hi Nicholas, firstly both are marvellous cars so you looking in the right place, but there were not huge numbers delivered especially in Australia so you are looking at a fairly condensed market which has kept the prices of 550 tight to the 575M as there are not huge aesthetic differences. As the guys have already said all 550's are manuals but only small numbers of 575M's. I believe there are only 69 RHD manual 575M's although someone might confirm if that was a global figure or a UK figure. Either way at this stage you won't really even see a manual 575M come to market.
Many including myself believe the manual to be the preferable Maranello which is not a slight on the F1 which is an excellent platform (although to get the best out of it you have to learn to drive it properly which won't come over night), but due to the mountain of torque coming from the big V12 making the manual so useable and entertaining in any situation. The manual in a lot of people's eyes is also the true lineage of Ferrari with the front engine V12, manual gated shifter and rear wheel drive.
As mentioned before, the 575M benefitted from technically advancements and this continued through its life span so a later one will have all the upgrades. Visually there is only subtle differences externally with most differences being internal, so these are in the eye of the beholder.
If you're not bound by having a manual try to find a late model 575M taking into account the three buying pillars....specification, condition and history. If they're all good then your onto a winner.
Current Fcars: 360 Modena
Gone but not forgotten: 360 Spider, 575M, F430.
Other stuff: '71 Holden GTS Monaro, '80 BMW Alpina B9, '74 Porsche Targa, Caterham, MB CL500, Land Rover Discovery.