Rose and Campbell at some point, are revealed to not be real. As I recall, this is before she tells Raiden that she's pregnant, so the person who says she's pregnant isn't Rose, it's the AI. At the end, they refer to the baby, so I guess Rose is psychic? Also, genuinely pregnant... And why was she there in the first place? Raiden probably rang her and said "Hey, just had a swordfight with a Spiderman villain, see you in five".
Speaking of Solidus, how did a gigantic nuclear-equipped... Submarine... Thing... That's full of ninjas and other nasties, not to mention all the Metal Gear RAYs, crash into a harbour in a populated city, whilst two weirdos in sci-fi outfits have a swordfight on top and nobody gives a fuck? This makes sense?
And how did Fortune protect everyone from the missiles at the end? And why? And doesn't she want to be killed anyway?
And that whole codec conversation before you fight Solidus is really bizarre. Raiden shares his name with a weapon? So what? Was he named specifically because of that? Why? And this consciousness that built up in the white house... How does this relate to Arsenal Gear and GW? That whole part is bizarre. Has Raiden always been working for this AI? How has he never realised? And if he hasn't always been working for the AI, how is he a part of the Solid Snake Simulation?
And what is the point in the Solid Snake Simulation? To create a super soldier? It seems like a slightly contrived way to go about it, doesn't it? And it doesn't even simulate anything. Raiden gains nothing from the experience. It cost whatever brain box put the simulation together an astounding amount of money. It cost them the Big Shell, Arsenal Gear and everything inside it, a bazillion dead guys... We're talking billions, easily! And Raiden comes out the same as he always was anyway!