I've just read Kare ga Megane o Hazusutoki and I really love the second couple. The seme is younger and he started out as a cute character and then after some time (puberty) he grew into the manly seme that he is. The uke isn't particularly feminine or anything either.
I'm more interested in how the seme grew from cute to manly. But I also like how both seme and uke are manly.

I don't run into yaoi or shounen-ai manga with this kind of couple often and I would love to read more about couples like this. If anyone knows any suggestions that would be awesome.

I feel like I need to explain my reasoning behind suggesting all of the following, but it's hard to do so without spoiling the character and couple development. The first two have seme characters that may not necessarily be labelled 'cute' but do become more mature as the stories progress. The second two do not detail the growth of the seme character (it happens between chapters), but they do involve the given transition of said character.

Bokura no Negai by Yamamoto Kotetsuko
Not Equal by Ike Reibun

Kawaii Akuma by Madarame Hiro Ai no Kotoba wo Uragaeshi by Abe Akane