Good recommendations here. Only French language texts. They are very clearly written, so if you understand any French you will be OK. But otherwise get the headphones. The video presentations do have English captions. Do watch as many of these as you can. Excellent museum, perhaps a little better on the Resistance than on the Deportation. Note: not a lot of English spoken at the front desk, either, so perhaps practice your request for headphones going in.
The best bouchon we found was Le Sathonay. Excellent in all regards.
I found Food Hall Paul Bocuse one of the more overrated places on the planet. A more enjoyable experience was on market days along the quais of the Saône. Art market, book fair, food market.
A more esoteric recommendation: The Museum of Printing. It has an appeal to the specialist, but it is very well done. The English language translations for the texts are excellent. Lyon was an early center of printing and the museum keeps up the heritage. Friendly folks, too.
A don’t miss: the Roman settlement / museum / etc above Vieux Lyon. Fun for the kids to take the funicular up the hill (and it is included in the Métro passes). The odeon and the theater are both well-preserved. You can simply walk around the area, no admission, no closing gates. Excellent view from there, as well. The museum itself is remarkable, if you have any interest in Roman civilization. The mosaics blow away anything held at (for example) the British Museum. Claudius’ bronze tablet is another example. The museum has an excellent introductory presentation on a relief map. In French only, but very clear. With kids, I’d pick and choose what I saw there. There are a few other things to do at the top of the hill as well. Pack a lunch (very nice parks with an overlook), a cafe, etc.
If you want some provisions for a picnic; Georges Reynon on Presqu’Île is a good stop.
General advice: hours of operations for many bouchons and even cafes can be somewhat limited, plan your meals out with some care.
Lyon has a BatoBus like Paris, don’t quite remember what they call it. Might be fun for kids and you get to sit for a while, too.
The Métro line up to Croix Rousse is its own line. I’m fairly experience with reading subway / metro / metra maps, and it confused me for a bit. You need to transfer to it, trains don’t run directly from one line to it. Once you are on that line you’ll understand why: it goes up at a steep incline, so they need different types of trains. Take the Métro up and amble down the hill, through the park.