As always, there's two sides to this. Lets take huge, muscular, gears-esque soldiers. On one side, they're tired stereotypes of marines being testosterone fuelled rednecks. On the other hand, I'd be willing to bet people would complain like hell if the COGs were built like the average Joe. Gears works because of the musclebound marines, not despite them.
Ditto for the sexy women. People complain that it's not an accurate representation of women, but yet I'd bet people would also complain if women in warfare were represented realistically (ie, in full plate-and-mail, full face helm, stocky and muscled, and covered in scars). Perhaps they wouldn't have as much rational basis for their compalints, but complain they would.
Steroetypes are stereotypes for a reason. Soldiers were musclebound. It came with the job. You spend hours and hours every day swinging a 4lb weight while covered in steel, chain and padding, and you're going to develop some muscles. Admittedly, the other two (girly boys - I'm looking at you, JRPGs - and scantily clad women) are less realistic and more fanservice, but hey, it's an imperfect world. Girly boys are there for the cute factor, women are there for the sex factor. Can't be helped. They're (as far as the marketing world is concerned) sure-fire ways to sell a product - cuteness for the female audience, sex-appeal and testosterone for the male audience, sexist as that may be.
The Japanese market, especially, seems to have built itself into a corner as far as characters go. They tend to be either feminine, sensitive teenagers, or massive 'MY NAME IS HUGE' warriors with appropriately oversized weapons. Exaggeration leaves very little room for a sensible middle ground.
And that, I think, is where most of the dislike comes from. Games are, almost by their nature, exaggerated. Exaggerated settings, events, characters; it all helps the developers to streamline the story so we can get down to the gaming. And while this may not be the best view in everyone's eyes, it is in those of the people who matter.
Stereotypical characters shouldn't be offensive, really. They aren't deliberate. They're shortcuts. We see a huge guy in some kind af armour and instantly we can recognise him as a soldier. We see some feminine-looking teenage boy moping around complaining and we instantly know he's the protagonist. Yeah, it's lay, but it shouldn't be offensive.
Well. That turned out longer than I expected.