(Game here is Parasite Eve 2)
It didn't happen in every game but often enough that it's noticeable. They're usually not shot as straight-up titillation, instead going for a tasteful nudity kind of thing and intended to fulfill some kind of storytelling or characterisation purpose
"You see, you gotta show them being vulnerable. They may be badass, but they're still girls, after all" 
-90s game director, probably
Kojima lost the plot with Big Boss When he fell in love with him making mgs3 or something. Giving him more fleshing out was good, but it seems to have been forgotten he was a monster who's philophy featured child soldiers as a very integral part of his society. It's like if the Star Wars prequels (as bad as they are, the example works) didn't have Anakin do anything morally questionable and he doesn't become Darth Vader by the end but the OT remains as is. You'd be like 'soooo..when did anakin become evil?'
You can, uhh... get a nuke that does something in the game's asynchronous multiplayer component. Nukes are bad, right???
I mean, being a non aligned mercenary state is in itself awful, but the game doesn't really get into that. Everyone you abduct into your service are just totally into it and it's only bad when they get sick. It's all just so stupid and pointless and damn does the gameplay wear off fast.
I fucking hate the existence of Cipher, XOF and the MGS4 twist with the Patriots actually just being the surviving characters from MGS3 instead of whatever the fuck MGS2 was hinting at. It sure is convenient that there is an unfathomably evil fictional clandestine organisation and a big bad for Big Boss and his ragtag group of heroes to fight. Thought things were about to get morally questionable for a second there!
Peace Walker was silly but at least the conflict was rooted in real-life factions and history, and the Cipher stuff was only brought back in during the epilogue after the main story had ended. 4 and 5 are just completely masturbatory anime scifi bullshit
Agreed. I had a lot of fun with Peace Walker cause it wasn't entirely up its own ass and the gameplay was great. Making The Patriots into the entire cast of mgs3 absolutely pushed the series over a cliff it could never come back from. Not only is it shallow and stupid compared to the less tangible patriots we got in mgs2 but it also just doesn't make any damn sense from a character perspective for most of em. Why the hell would SIGINT give a fuck about any of this? Same with Para-Medic.