The Analyst has almost complete control of the system in The Matrix Resurrections, so why does he call Neo and Trinity expensive? First released domestically on December 22nd, 2021, The Matrix Resurrections transports audiences back to a much-changed simulation inhabited by several new artificial constructs from the machines' world. One such program is The Analyst (Neil Patrick Harris), the creator of the current iteration of the Matrix and the chief architect of Neo (Keanu Reeves) and Trinity's (Carrie-Anne Moss) survival following the events of The Matrix Revolutions.
Midway through The Matrix Resurrections' runtime, Neo approaches Trinity at the garage where she works, hoping to wake her from the simulation. However, before Neo can get close enough, he is stopped by the Analyst, who delivers a monologue via bullet-time on how he came to be the singular director of his version of the Matrix. The Analyst explains that the machines used an extreme amount of technology and resources to revive Neo and Trinity for use in their new Matrix, with the Analyst sneering at Neo, "Do you know how expensive it was to keep you two alive?"
With this in mind, per Neo and Trinity expensive in The Matrix Resurrections due to how much energy it took to revive and restore their bodies within the Matrix. Throughout each of the Matrix movies, the franchise establishes that the machines only rely on one resource to survive: energy. This, by extension, means the machines' reserves of energy are their only true weakness, with The Analyst, therefore, implying that the machine war was a direct result of keeping Neo and Trinity alive.
The Matrix Resurrections establishes big canonical changes to the machines' narrative, with the machine war after Neo's death eventually ending the idea of humans versus machines. Instead, in The Matrix Resurrections, there are instead groups of humans and machines co-existing, with the only battles in the Matrix now centering on ideals rather than an arbitrary division of human or machine. Bugs (Jessica Henwick) elaborates on this change in ideological stance as she catches Neo up to speed on the new Matrix, stating that the machine war came about because the machines' power plants stopped making enough energy to sustain all life, "redefining what our side meant."
Although initially appearing as a throwaway line, Bugs' of the machines' recent history is given stark context by The Analyst calling Neo and Trinity expensive. It is therefore inferred that the machine's energy crisis may have been a direct result of them diverting resources and energy to preserve Neo & Trinity for use in the new Matrix - with the machine war starting at the same time The Analyst finds Neo and Trinity canonically. This, in turn, depicts an interesting evolution of the machine's ideals, with the Analyst stating in his monologue that he needs to make the "Suits" happy, indicating that over time the machines have become victim to the same base desire of greed humanity struggled with before the blackening of the skies.
This change in ideology is likely the catalyst behind why The Analyst felt the need to find an alternate energy source in Neo and Trinity sixty years prior, with their survival coming at the cost of a long and brutal machine civil war. While Neo and Trinity's revival eventually allowed the Matrix to triple the efficiency of its previous model, the pair were still no doubt an expensive gamble by The Analyst that paid off prior to The Matrix Resurrections beginning.
