Well, I didn't get any suggestions for my trip, but we had a great time! I'll post what we did for anybody else looking for family-friendly tips:
Day 1: We parked at the visitor's center and walked around the Market. We stopped in at the Aiken-Rhett House and did the audio tour there: that was great because DD could be noisy but we could make sure we weren't in the room with other people, so she didn't disturb them. Then we took a carriage ride (DD loved all the horses!) and grabbed lunch at Hyman's. Hymans was not too busy, but it's very laid-back: the kid's menu items came out right away, and they also brought a coloring placemat and a box of crayons and gave DD a coupon for free ice cream downstairs. Then we went the the battery and enjoyed walking around there.
Day 2: We went to the Drayton House, which was both a hit and a miss. We had to beg out of the guided tour because DD was being too noisy, so we let her run around the gorgeous grounds for a while and then rejoined a later tour. We also toured the gardens and got some great pictures. We ate at Sticky Fingers: great food, nice coloring book for DD, but she was feeling cranky so we got the food to go and hit up the hotel pool instead.
Day 3: Charles Towne Landing was fantastic. We all enjoyed the museum and the grounds, the mini-zoo, and the history walk. This is a great place to go with kids.
Notes for other parents: It is gorgeous to walk around downtown, but the sidewalks are uneven and hard for young toddlers to walk on. (DD scored some scraped knees.) The historic homes seem kid-friendly (we called ahead of time to make sure it was ok to bring DD), but the audio tours are way better than guided tours with chatty kids. Also, sure to bring a baby carriers since LOs can't touch the furniture/walls, etc.