1. In the original comics, it was made very clear that Peter, with the exception of his extraordinary intelligence, was a relatively ordinary guy, someone who you would think could never be somebody special in a million years. In fact, you could say that Peter is very much like the skinny dweeb in those old Charles Atlas ads--the guy who, in spite of how smart and charming he is, always loses the girl to dumb beefcake who takes pleasure in kicking sand in his face. His suddenly being bestowed great power is a simple twist of fate, and the original origin makes the point, to borrow from Batman Begins, that "it's not who you are that defines you, but what you do." What this new origin, if accurate, does it make Peter essentially the "chosen one," someone who is "destined for greatness" at the start. Not only is this something that is very overdone nowadays, but the downside is it implies that, it's not the content of your character that makes you special or great, it's your genes, your family, or background that determines your greatness, which is completely contrary to what Spider-Man is about.
Yes, I don't get where people have come up with the idea that Peter was experimented on, nor why - if it's true - it somehow undermines WHO Peter is and WHAT makes him special.
Let's say his Dad DID messed with his DNA...so what? How does that change his character? How does this change the fact that he's a smart, nerdy, shy kid who gets spider powers, and uses them poorly before learning to use them responsibly after Uncle Ben's death? It's not like he even KNOWS that is what happened and walks around school with girls swooning over him because he has super genes.
People seem to be hanging on the fact that because his DNA being messed with changes Peter because now instead of "anyone" being able to be Spider-Man, now, ONLY Peter can.
Guess what?
ONLY Peter can be Spider-Man, regardless of what's in his DNA prior to the spider bite. It is PETER'S personality, his life lessons, his desire and his mistakes and need for repentance that MAKES Spider-Man. It has NOTHING to do with his DNA. And remember, it the comics, he learned of the Spider-totem, which is pretty much a mystical version of the dad-messing-with-his-DNA angle.
2. In a related matter, it forces Peter's motivation become less about making amends for being culpable in his Uncle's death and trying to live up to the lessons his Uncle taught him and more about finding the truth about what happened to his father and living up his father's legacy. Sure, we know Uncle Ben's death will be a key factor in shaping who Peter becomes, but the trailers and even the filmmakers suggest that this will not be the driving force that makes Peter do what he does in the film. It's all about the "mystery" of what happened to his parents, instead, essentially turning Spider-Man into a carbon copy of Clark Kent from Smallville.
People can have more than one motivation. It's his desire to learn about his parents that starts the ball rolling. This does not take away from Ben at all. In fact, to me, it seems like it will help ACCENTUATE Ben's importance. Being obsessed with his parents might cause a rift between Peter and Ben, which would be a much more believable, and dramatic version of the little fight that Peter and Ben had in SM1. Upon his death, Peter will realize that by obsessing over his parents, he did not appreciate Ben.
3. It adds one more coincidence on top of an apparently ever increasing number of coincidences that are being set-up in the movie. Consider what we know already: Peter just happens to find his dad's briefcase and discovers he works for Oscorp, where he just so happens to be bitten by a spider which gives him powers. Gwen Stacy, the girl Peter has a crush on, also just happens to work at Oscorp. So does Dr. Curt Connors, who not only turns out to be Richard Parker's friend and colleague, but someone who will also become the very first super-villain Peter will battle against. Then there's Gwen dad, who not only apparently will go after his daughter's boyfriend but who, I imagine, will also be killed by the Lizard in the climax of the movie. And, of course, you've got the head of Oscorp, who it's probably safe to assume had something to do with the disappearance of Peter's parents, but also becomes Peter's arch-enemy that eventually kills Peter's girlfriend, and who has a son will also become Peter's best friend.
Stories are full of "coincidences" if you want to look at it that way. But really its as simple as cause and effect. One event leads to another, which leads to another, etc.
4. Unless otherwise explained, it potentially creates a big plot hole. Basically, when experimenting on his son, Richard somehow knew that, one day, Peter was going to find his missing briefcase, which would conveniently have his ten year old Oscorp ID badge and extra glasses which would still allow Peter to get inside the main Oscorp building and pass for his own dad, and, upon exploring, just so happen to find the very room containing the spiders in which one of them just so happens to bite him which is the very thing required to activate his dormant powers.
Heh, you should be in the Olympic Long Jump competition, because that was one of the biggest jumps to a conclusion I've seen lately.
Ignoring the fact that we have NO IDEA if the rumor concerning Peter's DNA is true, there is NOTHING that suggests Peter getting bitten was some elaborate design by his father. ALL we know is that Peter's parents left in a hurry and were never heard from again. Plenty of stuff would have been left behind. The suitcase is a plot device - nothing more. Its what starts Peter's desire to find out more about his parents.
5. It needlessly complicates what used to be a relatively simple, easy-to-explain, one sentence origin: "Peter Parker gains super-powers after being bitten by a radioactive spider." Compare that to "Peter Parker gains super-powers after being bitten by a gentically-altered spider created by his dad which activated long-dormant mutant DNA that was the result of genetic tampering by his dad."
The second sentence doesn't change the first. The second sentence - if true (which again, we have no idea, and I've yet to see any evidence that supports the hysterics) - does nothing but add a little bit more story to the event, it fleshes it out. It can still be easily explained as "Peter Parker gains super-powers after being bitten by a radioactive spider." because that is STILL what happens.
6. Unless it gets properly clarified, it doesn't get around the fact that Peter's father was conducting human experiments on his own son without his son's knowledge or consent. Not only is this unethical, it's tantamount to child-abuse. So why should we, as an audience, care about what happened to a guy who, for all intends and purposes, abused his own son? Basically, it sabotages the mystery the film wants it's audience to be as emotionally invested in as Peter himself.
Once again, we have no idea if this is true, and therefore we have no idea of the context of the rumor. I would agree that if his dad just came home one day and decided he wanted to dick around with his son's DNA, that'd be a problem. BUT not knowing what the context is - why he did it, and what, exactly did he do if anything - doesn't allow us to judge his actions. Even still, I, as an audience member, WOULD care about Peter uncovering the mystery, because I WOULD want to know why.