As discussed above, sci-fi isn't necessarily meant to be logically coherent, it's just really cool when it at least has parallels to reality and has an aura of logical coherence.
Not to poke wholes in anyones critisisms, but the problem with critisizing anything that involves sci-fi technology interfacing with human biology (what the Matrix is doing) is that you can come of up with a number of half baked excuses that might fit. It only becomes an issue where there are contradictions.
For example, in the Matrix, we don't, IIR, see what everyone is doing within the Matrix. Sure they could be living their everyday "lives" but that's one of the criticism the Matrix holds on society itself. Are we actually living our life or surrendering it to something that can extort and exploit us out of fear?
Neo and a select few people regain their autonomy for whatever reason and do their own investigations (the Matrix knows this) Everyone else seems to be content with fulfilling or suffering their role within the Matrix. In real life that may be a parallel, and if we want to be on the nose, corporations do operate on a need to know basis and are suspicious of people that ask lots of questions, so for all you know the person in the cubical next to you is doing some complex research the Matrix wants them to do.
Of course, why not build a net of neurons that can do work? Well, for starters we don't know if such intelligence is impossible without some sentience. The question of "why" might be mandatory at some level of judgement in order to make future decisions, and certain attachments to certain judgements and data is not necessarily something that is unintelligent. But then we wouldn't have a narrative device that appeals/are relatable to real people's emotions.
The Matrix has enslaved humanity is what is important. Talking about how, does yield a useful conversation, and why is also important, but everything in between is creativity and focus grouping.
Expanding on how, and why, the Matrix posits: Through isolation and illusion, because we wanted to maintain our supremacy over machines.