I understand how your perspective on things can change over time. Here's my 2 cents:
No. Bella is still a teenager - this is important to get. Teenagers have not yet had enough practice to be as tough as they would like to be. As a matter of fact, you can see Bella's toughness grow and evolve over the course of the books. But Bella is plenty tough for her age, accustomed to independence within the world she is familar with. She operates independently in Phoenix and Forks - not in Italy, where she doesnt speak the language or even have a map. Certainly not in Volterra - like the rest of us, in unfamilar territory she needs guidance, and there are no guidebooks for Vampireland. She falls in love, but she is not dominated by Edward - as a matter of fact, despite his unfair advantage of being supernatural, she fights off his influence much more than the other humans around him. She asserts herself often, from the very beginning. She is not a weak character -- it is not her fault that she is not as fast, etc, as the supernatural characters that she chooses to surround herself with. A real person is not less strong of mind, merely because they hang out with others who are even stronger-minded.
No. Edward is overprotective. There's a difference. He is so overwhelmed by Bella's COMPARATIVE fragility that he overreacts, which she tells him, except when she uses his overprotectiveness to manipulate him. His apparently overcontrolling behavior at the beginning of Eclipse is readily explained when you look backward from Breaking Dawn. Edward is familar with European werewolves, which are very different and even more dangerous than the Quileutes, and slowly comes to realize that they are not the same. And then, from an early point, Edward tries to make everything about what Bella chooses, even though his anxiety sometimes leads him to want to overrule her choices.
By the way -- when you look at the books, I think saying both that Bella is weak and Edward is controlling/abusive completely falls apart.
No. Jacob is even younger than Bella, and though he goes through that rapid physical maturation, he doesn't seem to go through a rapid emotional maturation. He starts off quite mature *because of his life experiences* - losing his mother, caring for his father. But he appears to have less experience with romantic relationships and hasn't had time to mature in his approach there. He kisses Bella against her will - once, no repeats. After lots of mixed signals beginning in Twilight and running through New Moon well into Eclipse. He didn't realize it was against her will - inexperienced romantically, and unable to realize through his own desire that she is trying like hell to get away from him. He said he was sorry. Jeesh.
ANYTHING can have a negative impact on ANYBODY. Go look at the banned books lists - some relatively reasonable person thought that each one of those would predictable have a negative impact on people who read them. Bet you read something on them, and here you are, writing papers for college. But books are not the ONLY impact on most people - family, friends, society have large impacts. I'm going through some heavy emotional stuff about mortality and the afterlife while reading these books - but its not Stephenie Meyer's fault and I'm handling it. Maybe I will be a better person for wrestling with this. That's what art is about, right?