These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Ho Yay: Almost everything Roger says in the third game is a not-so-thinly veiled come-on to his "best bud" Kohtaro.
Parodied with the Roger and Munchausen team-up. Their dialogue can be heard here.
On the other end of the spectrum, Mihee and Reika's team-up scenario ends with Mihee straight out declaring she'll take Reika as her wife, with Reika putting no more opposition than a complaint that she doesn't have the legal age to drink yet when invited to.
Macekre: When the first game in the series was released in the U.S., it was released under the title Mobile Light Force 2, with the implication that it was a sequel to a completely unrelated game (said game being Gunbird). The same localization team got a chance to do things right with Shikigami II, and that time they left the characters and setting intact, though still with a very dodgy translation.