I think the two best museums are Ancient/Modern Art and Bozar. But others might say Musical Instruments and Magritte. Because they're a different part of town, and I have no interest, I skipped the EU Parliament and the Atomium. Note that there is so much within walking distance of the Central Station (NOT the Midi/Zuid station you'll be going to. But your ticket takes you, once, for free on the local trains to the other two downtown stations. And on the way home.) Do some figuring to see if you want a one-day Brussel Card for certain museums and transit.
Other good museums, Coudenberg palace basements, the nearby History museum (which doesn't pull any punches about the Belgian Congo.) Petit Sablon park and fence sculptures. Many pretty churches, and the Cathedral has a lot of interesting war plaques and memorials inside. I think the Rue des Bouchers restaurant street has some charm, but you have to be ready to dismiss the AGGRESSIVE touts trying to get you in to restaurants that are widely reported to abusively pad the bill. Do not eat on the Rue des Bouchers. If you insist on Mannekin Pis, keep walking to see the female version, supposedly paid for by restauranteurs wanting tourists to have a second stop. (Similar but much better sculpture by Kiki Smith, http://www.groundsforsculpture.org/Artist/Kiki-Smith )