Bit of an apples and oranges comparison! The condition of the example you buy is going to be a far better indicator of reliability than the mechanical merits/build quality etc. All cars of that age are susceptible to rust-bodywork rust is trivial, it's the undercarriage, inner wheel arches, sills etc that matters-and that sort of corrosion is easily hidden.
Both cars are mechanically simple and ubiquitous enough to make finding parts fairly straight forward.
Both the rear mounted air cooled flat 4 and the water cooled front mouted I4 suffer from a common problem-inconsistent cooling which can cause overheating. Never lug an air cooled engine! You either love the noise of the fan or you hate it. Mini gearboxes are a weak point. Mini is nicer to drive, Beetle is more spacious. six of one, half a dozen of another.
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