I'd say if theres nothing between the two cars when you see them (ie assuming that one isn't a dog where the other is fine..)go for the manual.
The auto box is well known for trashing its thrust washer (replacement 'box time) - the box on mine went at about 88k (previous owner had a second hand box rebuilt and installed).
Don't know of any issues other than obv having to replace clutches, but I'd say the driving experience will be better with the manual, and you'll get marginally better consumption.
But I'd say go for the auto every time. There's 150 000 miles on my car & the thrust washers in the gearbox are still where Vauxhall put them. The driving experience is far far better for me without fannying about with 3 pedals.
I can think of issues with manuals. There's been a few requests here for another dual mass fly wheel. They're only about £800 a pop new.