Thank you for the comment!
I agree the Matrix RPG doesn't have experience levels and rewards that would work well with a long campaign. I have found it works well for multi-session stories where I tell a story over 3 to 5 missions. When I have tried run a campaign it didn't go over 3 months.
Currently I am working on version two of the Sourcebook that adds "The Machines" as playable characters. Hopefully finish in a year.