It's always been a belief of mine that everything exists in balance. Good and evil, up and down, ying and yang, black and white. For something to exist, there must be something to counteract it. That is just how the world was made, and this delicate balance is necessary for everything to function.
Stop thinking about it as freedom from the Matrix of being stuck in it. Think of it as a choice between being an ordinary person or being able to make the laws of physics themselves bow down to your very control.
With every great gift, though, there is a sacrifice. This is where the balance comes into play. At the cost of being able to break the rules of reality in one world your condemned to live and reside in another. A dark, dystopian world where your life is always in danger. You are never truly safe and never feel as such. Whenever your able to enter your former world, The Matrix, your never able to actually enjoy being there as you once were. Every time you enter that world you do so with a purpose. That place you used to love and live in becomes a war zone, nothing more.
That is the real choice. Either live in the world you do and be completely unremarkable or become a god within it but be exiled to another world where death could claim you at any instant. It's a normal life or extra-ordinary power. You can't have both.
If those are the two choices I would choose the red pill and would take the power to bring about change at the cost of losing everything else. It would be a heavy price to pay, but a worthwhile one to be able to create a better world for everyone that I know and love.