I just read Wild Adapter and fell in love with the two main characters. I love the innocent Tokito and the protective Kubota. Are there any other shounen-ai/yaoi manga like that?

Another example would be like Kai and Hal from Switch.

The uke would have to be the outcast of society kind of like Tokito. The uke's different, something happened to him in the past (something like experiments were performed on him as a child). He is hesitant on trusting the seme upon meeting him. I guess basically, the uke acts like a stray animal with special abilities. People are out to capture the uke so they can use him for their own gain.

The seme is protective of the uke and rescues the uke.

Sorry if this is vague. I'm just really into these types of story plots.

Thank you so much! 🙂

BrandNewWings

Jinjuu Houretsuden maybe?

Been a while, but Silence (AKIYAMA Koito), chapter 7, may fit.

Mori no Koe - the first story, and possibly the others too.

Asterisk, Moon Trick and Get Backers might fit. Also Taiyou no Romance.

Most Morimoto Shuu are like that.

Maybe you find more with the 'Protective Seme' tag:
http://www.mangaupdates.com/series.html?category=Protective+Seme