Both of these mangas have similar characters and similar story styles. In both Delinquent styled males leads meet some rather odd girls.
In fact they are nearly twins in the sense of the character styles and story set up.
However I believe Bokutomo to be the better of the two, as the characters are stronger and the story is more down to earth. Im sure if you liked one you'll at least be amused by the other..
When I was reading Kanojo ga Flag o Oraretara, I couldn't help but notice how much the stuco prez reminded me of Chiiko from Fujimura-kun Mates. I'm sure those series have more things have in common than one similar character and funny jokes, but I can't quite name them. Nonetheless, if you liked one of those two manga, odds are you might like the other one too.
Both Fujimura-kun Mates and Mission! School are gag manga with brutally hilarious punch lines. In both, the humor is also delivered by characters honesty (you know, les enfants terible kind of thing). Not to mention that the girls in both of those series seem to be lacking a great deal of common sense. If you liked the humor in one of those manga, odds are you might like the other one as well.
After being separated for six years, twins Akito and Akiko Himenokouji have joyously reunited and are as close as ever - in fact, maybe a little too close for Akito’s comfort, as his sister has developed an unrestrained brother complex! Though her brother doesn’t take her lustful feelings seriously, Akiko is determined to set the record straight with the other ladies around him, including the three other beauties that live in his dorm and want the boy for themselves. Every morning, noon and night, the girl continues her mission to cross the line with Akito, and she won’t let any girl or sense or morality get in her way - for as long as there’s love, it doesn’t matter if he’s her brother!
Both series revolve around a guy who's fending off abnormal girls. The comedy in both series comes mainly from the male lead doing tsukkomi. If you love good tsukkomi, you should definitely give those two series a try.