I actually felt that T3, while inferior to the two Cameron films, was actually quite close in tone to the original Terminator. Both films basically dealt with people unable to escape their destinies, and try as they might they could not alter the future. It was only T2 that had the touchy-feely message that the future is not set in stone, and if we're all really nice to each other we'll be a-ok.
As for John Connor, I don't know what the big deal is with him being a scared kid. The John Connor of 2003 is not the same as John Connor of 2027. Why do some fans labor under the misconception that all characters must remain absolutely static, and cannot be portrayed one iota different from their previous films, particularly in respect to anything that's a "prequel." It's called character development people. Look it up some time.