Can't help regarding the autobox, but my wife had a couple of R56 Cooper S's and a good mate works at Plant Oxford and has had a hew MINI's on their employee scheme.
Putting engine choice to one side for a moment, the first thing is that spec's of used cars vary wildly due to the wide range of options available. Personally, I'd look for one with the Chili Pack as that includes lots of things you'll probably want (it'll make it easier to sell later, too). The standard audio system is, imo, feeble so if "reflexgirl" (
) likes her sounds, look for one with the audio upgrade. The Visibility Package (auto wipers, etc.) is nice to have too, and if you're lucky you might find a car with heated windscreen as well which is good if the car lives outside. The chrome trim packages (both external and internal) brighten the car up a good deal. The Automatic Climate Control didn't work properly on either car my wife had (both from new, both had multiple dealer attempts to fix it), so I wouldn't bother with that. Avoid anything with Sports Suspension if it's on 17-inch runflats. On anything other than billiard-table smooth surfaces it redefines the term "pain in the a*se" and makes the car very difficult to place accurately if pressing on on bumpy roads.
As far as engines go, both petrol and diesel seem to be ok, but the Dooper can achieve 60+ mpg with ease and is pleasantly torquey.
Other than that, despite the car being very similar in outside dimensions to a MkIV Golf, boot space is very poor and the rear seats are cramped. There's no doubt that they can be fun to drive and reasonably cheap to own (an 09/10 car will still have 2 or 3 years of free servicing left if the original purchaser took the TLC package), but if practicality is needed I'd look elsewhere.
BTW, if you haven't found it yet, the
MINI2 forum is a good resource.
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