I didn't mind it. They had to top the T 1000, so a machine that can control technology seemed like the next logical step and a unique "power" for the T-X, given than the previous Terminators had a unique gimmick. I also think it was fitting that the first female Terminator could "manipulate" other machines. It's a quality that has historically been given to femme fatale characters in films.
Also, her ability to control machines had a payoff when she reprogramed the T 800, and he had to shut down, kind of like he shuts down in T2. They could have done a bit more with it, but it was nice character moment for the T 800 to struggle and do the right thing, without betraying the integrity of the character. He didn't shut himself down because he felt bad...
Yes, I'm not a fan of the depiction or actor playing John Connor. However, the whole point of the film series has been to protect the savior, the man that's going to save the human race. The first and best film (in some people's opinion), never tried to stop judgment day, it was going to happen until T2 changed that, but T3 brought it back to the first film and in the end John had to survive. He could have been a better character in T3, but oh well, at least he didn't become a lame villain or got killed and replaced by an even worse, less believable girl in DF.