Clannad being the first VN I’ve read, my memories of it are slowly merging with memories of the anime, so I’m not sure about all of this, but I’ll try to recall some differences.
In order to awaken the “cool” side of her onii-chan, Mei tried to make Youhei to worry about her. Tomoya assisted her with that. In the VN, their means were more provocative than in the anime, which made Youhei’s reactions even more disappointing at first and more touching in the end.
First of all, Mei needed a place to stay while visiting the city (I believe she ended up staying at Nagisa’s place?) and Youhei didn’t know where she did. So Mei kept it a secret at first. He didn’t seem worried, though. She also told him that she’s visiting her boyfriend who lives in this city. Still no reaction.
Later on, she “revealed” that she’s actually staying at Tomoya’s home. She also said her boyfriend is in fact Tomoya. When the desired reaction didn’t occur, Tomoya went even farther and spouted some dirty-old-man-lines at Mei like “make sure to wash yourself thoroughly today”, but Youhei still didn’t get worried or mad (Youhei’s trust in Tomoya seems so boundless it’s touching).
I think it was around that time that Tomoya gave up on him. But Mei still persevered and dragged everyone into the whole soccer team thing
Additionally, over the time of her stay, Tomoya had several date-like events with Mei. Though there was no explicitly romantic development, the ‘mood’ of those events and the route itself could be interpreted in both ways.
