I still think people are making this to be more complicated than it needs to be.
Pre-X-Men: Xavier recruits Jean Grey for his school. He realizes the potential of her powers, and to prevent it from overwhelming her to a point of inability to control it, he puts the psychic blocks in place in her mind. Isolating Jean's powers to her subconcious mind, where she can't unleash them, creates a dual personality within Jean's mind. The concious Jean... the regular, normal girl. And the subconcious Jean... that wants this power.
X-Men: During the Liberty Island incident, Magneto's machine affects Jean. For a machine that has no affect on mutants, why her? What makes her so special? These mental blocks. These blocks are broken with this machine.
X2: With these mental blocks broken, Jean now has access to this power... as seen with the awesome displays of power with the missles, and during the breaking of the dam. Why hadn't Jean become "Dark Phoenix" here? Because, though she had access to these powers, she didn't reach for their full limit. Only stints, in which the Phoenix hinted to manifest itself (firey eyes, etc...). However, her concious mind was still in control. After she leaves the jet to save the rest of the X-Men, she reaches deep and pulls out the full extent of her power, to save her team. The Phoenix is unleashed.
X-Men: The Last Stand: Jean was overwhelmed by the rushing waters at Alkali Lake. Her powers wrapped her in a cocoon of telekinetic energy, but essentially, her concious mind was now gone. Any resistance from the past from these mental blocks, or Jean's conciousness, to supress these powers and the Phoenix personality was now gone. What's left of the real Jean called to Scott, because she was still alive. But after she rose, the Dark Phoenix took over, and killed Scott. Unlike in X2, where it was Jean Grey wish flashes of the Phoenix, Jean Grey was gone, the Phoenix had taken over, and it was the Phoenix with flashes of Jean Grey.
In X2, her conciousness was able to tap into her full potential because the blocks were broken. That's why she's "good" Phoenix.
In X-Men: The Last Stand, after "dying", her conciousness is gone basically and the dark side can take over. That's why she's "dark" Phoenix.
It makes total sense, and I think we're making it more complicated than it needs to be.