If you want to see Semuc Champey the best way would be a shuttle from Flores to Lanquin and then from Lanquin to Antigua. But these are long shuttle rides (8 hours or so) so not sure if your kids would be up for that. I like Lanquin and Semuc. But you do also have to take a very bumpy ride in the back of a pick-up truck to get from Lanquin to Semuc. One day for Semuc is enough but if you have a hotel on the river a second day would be nice for relaxing and swimming. Chocolate making workshops are also offered.
For Antigua: I am sure exploring some of the ruins would be fun (La Recoleccion is impressive, Las Capuchinas...). The kids would probably also like both the general market and the artisans market. There is the ChocoMuseo with chocolate making workshops. Maybe a coffee tour (Filadelfia comes to mind but there is also La Azotea in Jocotenango). The Valhalla macadamia nut plantation is fun too.
The lake: visit the different villages by boat (don't miss a visit to Maximon in Santiago), hike from Jaibalito to Santa Cruz (45 minutes), the nature reserve in Pana (nice hike with hanging bridges, waterfall, monkeys, coatimundis, butterfly garden), chicken bus to the market in Solola (Tuesdays and Fridays)... San Marcos also has a small nature reserve. I have not been there but I believe it has a few trails and is good for swimming.
Xela: the volcanoes are too hard with the kids but there are also scenic hot springs (Fuentes Georginas). For Laguna Chicabal (crater lake) you would have to get up to the entrance first as the walk from the village is quite long and steep. There were pick-up trucks. From the entrance it is maybe 1 km to the viewpoint. There are steps down to the lake and you can walk around it but you have to climb back up of course. There are also Maya villages and markets near Xela.