@Bakker look through the danmei room. You might find something there maybe? http://forum.novelupdates.com/threads/danmei-room.1199/
Seme is for http://www.urbandictionary.com/define.php?term=seme ( was to lazy to rewrite the definition)
Hmm...don't think I've chanced upon a seme protagonist novel for now...Most of them are ukes... Oh, but if you don't mind visual novels, then I'd totally 100% recommend 'No Thank You!!!' Haru is such an amazing seme~ >y<
Feng Yu Jiu Tian - you wouldn't expect it, but yup. And if you haven't read it already, Captive Prince is the best!
Spoiler The first time they had sex, Feng Ming was the bottom. However, it was extremely painful for him and they stopped partway. After that, Rong Tian suggested that Feng Ming top until his body is able to take being the bottom. From what I remember, the manhua is pretty loyal to the novel (albeit heavily condensed), but since I haven't read most of it, I can't say for sure. Rong Tian and Feng Ming have a lot of "foreplay" type scenes in which Feng Ming is the submissive party. It's just the actual sex in which Feng Ming is the top. From what I can tell, the author intends for Feng Ming to be a submissive bottom type of character (eventually), as she barely describes the sex scenes at all when Feng Ming tops.