Not really. The machine's motive might not make sense to us humans, but machines don't think like humans. It's basically an unintended side effect of how the human programmers wrote the program. If there's a glitch/design flaw in the program, the machine's motive could be anything.
The action an special effects were not the only thing that made it good. It's a very interesting premise and the way the movie gradually revealed the truth made it fascinating to watch for the first time, to me anyway.
So, I agree the premise of a world within a world is a very good one. Its the motive for the machines creating and maintaining the world makes no sense! It sounds like you've hand waived that one with a "the machines work in mysterious ways" to me.

The movie spends a fair bit of time describing how its all about energy, how the energy is harnessed but the moment you think about it...this happens:
Of all the species on earth, humans have the least efficient biology and give off enough heat to collect and power machines?
Also, liquefying humans and feeding them back for "infinite energy" violates the laws of thermodynamics. It's just silly.
It just doesn't make any sense logically. Even if maintaining a bunch of animals to harvest their body heat and electrical impulses wasn't a net energy loss, humans would be a terrible choice. Why didn't they fill the matrix with cows? Or at least lobotomize everyone so they were easy to manage. Or a bunch of clones of a genetically engineered beast designed to be more power efficient. The vast majority of life on earth gets its energy directly or indirectly from the sun anyway, so humans are just really inefficient solar power. And what about all the cpu power they need to run the virtual world?
And then the third movie screws this up even more. Apparently if you fly high enough can get above the clouds...and if there's no sun, why isn't it pitch black outside? Solar panels still work when its cloudy. Why don't they use orbital solar satellites and microwaves?
If the machines are hiding some other further motive, the humans are pretty stupid because none of them even seem to question why a bunch of super intelligent robots that essentially defeated them are using the crappiest power plant in the universe on a resource starved planet. What really stinks is they could have replaced the nonsensical situation with an "its all ruse" reveal in the later movies. Nope, they doubled down on the unbelievable motive in the end.
I still liked the movie of course, because it was so exciting the first time you kind of didn't care to much. And the first one had some fun paranoia sequences in the beginning that were fun.
The motive for the machines has to be changed for the plot to be really solid. I think the machines using the matrix as a cluster computing system would be plausible. The machines recognize they aren't capable of imagination or true invention so they plug a bunch of humans into a fake world and record their thoughts. Perhaps the machines were being badly beaten in the war because of the human capability to improvise and innovate until the machines built this system and defeated the humans. The human brain battery is like a coprocessor they use to make up for a deficiency in their design. And the whole thing runs on uranium, solar and geothermal power because derp.
Even the matrix within a matrix idea suggested earlier is better. At least then Neo doesn't have magical powers in the real world for no reason.