These places are packed. Packed with people, and packed with things to see. The crowd in front of the Mona Lisa is ridiculously large all the time, and overwhelming for adults let alone the children.
Before you travel, visit the website for any of these museums, and identify all of the exhibits that you really want to see. The websites usually have floorplans, so use them to map out the location of these exhibits. There are often online "collection highlights" guides so you can see what the best exhibits are - particularly useful if you know nothing about the museum before you go.
Aim to see the exhibits on your list, but keep an eye on the ones you pass on the way. These will be bonuses you can add to your experience. We had a very small 'hit list' for the Louvre, despite being art-aware: the Mona Lisa (a bit cliche, I know, but it was our first visit), the two Slaves by Michelangelo, and the Nike of Samothrace were the top three. Connecting them, however, we discovered the Coptic Gallery, the Greek red- and black-figure vases, ancient sculptures, and European painting from the Renaissance.
The Louvre contains many other glorious exhibits worthy of further exploration, but we saw those things most important to us, got in a few bonuses, and got out with no complaining from the kids.
A similar technique worked well at the Metropolitan Museum of Art in New York, but we failed to use it at the Natural History Museum and boy did I pay for it with the whingeing...
Wandering aimlessly, especially with kids, is a certain path to mental instability. It might start out as fun, but it won't end that way.