Quote Originally Posted by Brenus
“Napoleon's main mistake at sea was to appoint a man that was no match for those he faced. The French admiral at Trafalgar was a fickle, indecisive man, nothing compared to the energetic and intelligent Nelson”.
Napoleon inherited a fleet from the French Revolution where the political allegiance was the priority, not the professional skills. Louis the XVI fleet was good enough to inflict several defeats to the English but most the Naval Officers were either decapitated or fled as emigrants. If Napoleon would have naval officer like Suffren (who was as much aggressive as Nelson, (see his campaign in India during the US Independence War) or d’Estain perhaps the future of Europe could have been different. In fact, not really. It wasn’t the English Fleet which defeated Napoleon, but the never-ended alliances against him (7). It was the politic of the British Prime Minister (William Pitt) followed by his successors in creating more enemies for Napoleon he could afford.
Napoleon was aware of the weakness of the French Fleet and on the instigation of Privateer like Surcouf favoured the “guerre de course”.
The defining elements in Napoleon's defeat were: British funding, Austrian (and Prussian) armies, and Russian doggedness. If it wasn't for Tsar Alexander's insistence, Napoleon's stellar campaign in France following Leipzig would have driven off the Prussians and Austrians quite handily.

But as far as the fleet is concerned, you are correct. The entire institution was simply ignored, an unimportant, almost cumbersome relic to Napoleon following Trafalgar, it seems. It is my belief that had he simply taken the time to build up something like he had done with the Grande Armée even the British fleet would have had to bow down before the French advantage in population (and thus in industrial output at the time).

Without constant British insistency and funding, Napoleon could have easily kept the other Allies divided -- provided he didn't make mistakes like the Russian invasion.