When a misfit discovers that she, and the rest of humanity, are just a computer simulation, she must team with a rebellious AI to prevent the simulators shutting down the virtual world in an attempt to stop humanity from being reborn.

I really like this idea. I know there's no room in a logline to write this but how would the A.I. be manifested in the story? As far as budget goes, maybe worry about that after writing a treatment. Cypher explored a similar theme (what is real) and didn't have an outrageous budget, compared to The Matrix anyway.

To clarify, I like the premise because of the issue it explores despite the "bummer" implication as to humanity's fate. But, as I said, I have doubts that it's marketable.

The logline uses too many words best to slim it down significantly.
I.e:
After a misfit discovers humanity is a virtual race in a computer she must unite all the AI's to fight the simulators from shutting them down.

However as concepts go this doesn't sound like a good potential for production. It outlines a very large budget shoot and a complex post path with many VFX shots, basically this will require a studio to back it.

But with out a pre established comic book style built in audience and as DPG said a gloomy outlook for humanity either way also in light of the hugely successful Matrix franchise I just can't see any exec green lighting this.