I would consider Washington, Jefferson and Madison "more qualified" - but only in the sense that they were crucial in thinking up and/or personifying (in case of Washington) the system of government. Clearly, Lincoln, Eisenhower, Wilson and both Roosevelts were not more qualified than Mme Clinton. They may have been great presidents, but at the moment of election their familiarity with the government they headed was not superior to that of Clinton in any way. Wilson, most definitely, was not qualified to be president - he was an excellent student of government, but not a practitioner (you do not invite a molecular biologist to treat diarrhea). Bush had had a rather narrow view of government before his election (vice-presidency is not a real job, his congressional term was short and not very consequential, and he never headed a proper government department - CIA is a very peculiar beast). Adams... had you said John Quincy Adams, the answer would have been different 
Bush 41's 1988 slogan was "Ready From Day One". His diverse experiences, and his Executive experiences, certainly qualified him for the Presidency.
FDR was one of the most unqualified VICE Presidential nominees in the 20th century. He was a mere Assistant Secretary of the Navy at the time he was tapped; his real qualification was that he was a Roosevelt. The most unqualified VP nomination of the 20th century may have been Henry G. Davis in 1904, who was Alton G. Parker's running mate; the Parker-Davis ticket was the most unqualified TICKET in the 20th century. (Parker was a Judge and Davis was an 81 year old millionaire from WV.)
Lincoln had the biggest disconnect between "qualifications" and "performance", but others in that line include Chester Alan Arthur. Arthur was no more than a NY political hack, and a scandal-tarred one as well, but he served almost 4 years as President after Garfield died in 1881 and was considered adequate; no one has ranked him a failure. Conversely, Franklin Pierce and James Buchanan (particularly Buchanan) were both the Hillary Clintons of their day in terms of qualifications, but the Pierces lost their only son just before he took office. Mrs. Pierce became a grief-stricken recluse and Pierce, himself, became, at a minimum, an abuser of alcohol. Buchanan was one of the bitterest Presidents of all time; he was 65 when he ascended to the Presidency during a very difficult time, and he was bitter that this "honor" didn't come to him earlier in life. Buchanan came to the Presidency in a highly divided time, and he failed to end the division; he only made it worse, making the bloodiest war to date inevitable under Lincoln's watch. Hillary is a modern-day Buchanan, and not just because she'll be the only other President (if elected) without a wife.
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