What you're missing is the difference in genre. Due to the fact that Rising is a hack and slash game it doesn't provide the developers with the same broad tools for gameplay/narrative that a slower, more ponderous game such as MGS3 might provide. Rising emphasizes quick combat and simplicity of control whereas most would say that MGS is rather lax in the cohesive combat controls department, thus Rising's gameplay has to present boss fights which allow you to use the game's primary mechanics effectively rather than creative solutions in order to triumph over them.
Mistral uses dwarf geckos to mob and immobilize you as well as her staff to overwhelm your defences, so you have to evade being surrounded and pick the right moment to sever her staff using Blade Mode to leave her vulnerable. Monsoon is impervious to sword attacks while his EM field is operational and makes quick decisive ambush attacks, so you have to master parry/counter in order to break his defences. Sundowner uses his blasting panels to protect himself, so you must master precision cutting in order to render him vulnerable and make the fight more fair.
While most would say that The End was more engrossing and I was more original, I think Rising's bosses perform quite well when compared to various other Spectacle Action game bosses. I'm certainly happy to put the duel with Sam above Nelo Angelo 3 on my list of favourite boss fights.
Also, keep in mind everyone, Platinum is more than just Kamiya. We're considering what the entire studio would do with the property, not just one man.