you just named the three places in Paris with highest concentration of tourists, if you're going on a weekend and don't like crowds avoid those 3 at all cost.
It depends of what you like, I would go to Musée d'Orsay, you can browse some impressive art quickly (not like a regular museum, where you are forced to go trough all the rooms) and you can stand at the top just by the Seine, after I would have lunch and take a stroll trough the Jardin du Luxembourg (an amazing garden where you can walk, relax, etc.) and then would finish the day at a cafe in Île St-Louis
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