Are there specific plot inconsistencies in The Matrix Trilogy?

Well, let's think about this, why are only humans used for the harvesting power?

Where are all the organisms? You know the ones that don't need the sun.

Morpheus: A singular consciousness that spawned an entire race of machines. We don't know who struck first - us, or them. But we know it was us that scorched the sky. At the time they were dependent on solar power and it was believed that they would be unable to survive without an energy source as abundant as the sun.

One could say that all organisms became extinct? But that's stretching it. The machines must have been smart enough to take some organisms with them and mass produce. Just based on logistics, you would be able to save on computing power to run the simulation. Seriously, the amount of 3D rendering that goes on in the Matrix must be a lot

Next part, everyone is all on the ship training Neo to be the one and all that so after Cypher talks to Neo and gives him the drink on the ship how in the world did he boot into the Matrix for dinner with Mr.Smith?

Was it someone else? No, because Cypher was on shift that night to monitor code on the Matrix. So let's say he managed to get in. Who got him out?

There are many more holes, I will have to watch it again to remember. Notice, this is all based on the first movie.

Now that I think about it, I think the biggest inconsistency - besides Neo suddenly gaining power in 'the real world' at the end of the second film - is the travel that Neo takes to get to The Architect in the second film, and The Architect's implication that this Neo is the 7th (or perhaps more - it's been a while since I saw the film) version to meet him. There are a few problems with this:

1. The free will of other people in each incarnation. Does this mean that in each incarnation, there was an incarnation of Cypher that betrayed his teammates?

2. The fact that each incarnation was Keanu Reeves. It would have made more sense to have 7 different people representing Neo on the screen, seeing as how Keanu Reeves couldn't possibly have been born the same way each time (in theory, if the machines had a copy of his DNA, I suppose this could be true, but this seems like a stretch even for the world of The Matrix)

3. The path that got Neo to The Architect. Neo interacts with a number of 'old' programs, programs that supposedly have been around during each incarnation of The Matrix. None of them seems to have learned anything from their interaction with Neo, and Agent Smith is radically changed in this incarnation. If each incarnation led a similar path to The Architect (with the only major difference being Neo's reaction to the nature of The Matrix and his choice of saving Trinity or restarting the whole process), then Agent Smith should have been somehow been able to retain his power from one incarnation to another (after all, it's implied in Matrix Reloaded that he's no longer part of The Matrix, but is outside of it).

The biggest one that springs to mind is the fact that he is 'all powerful' within the matrix by the end of the first film, and actually stops it from running. Then in the next film he's just quite good at fighting, but not really omnipotent like in the first film.

For me, the greatest inconsistency is the Neo with superpowers at the end of the second movie in the 'real world'. It's a cheap trick that breaks the matrix own rules with the universe showed in the first movie.

Well, I was very much convinced with the first part and even the second part for that matter where the version of matrix gets upgrading. In fact the Viral concept of Agent Smith could not have been depicted more appropriately. But hell broke loose in the third part. I personally prefer they never took it.

Neo being blind and having a vision in the live world is totally out of context and can be called as "nuts".

Well I think this trilogy suffers from many problems that stem from the fact that it was never "planned" to be a trilogy. Like many other movies (Back to the Future, Pirates of the Caribbean etc.), the first movie was written as a standalone story without any purposely created plot holes for future explanation. What this means is that additional story telling based on the first movie will have to be then "made up" on the spot and tacked on to the original story. While there aren't any severe inconsistencies, many viewers can tell that many sequel story elements might not necessarily fit with the tonality of the the original. This in itself could "turn off" many fans to the sequels of these films.

This of course isn't specific to just movie though. The same can be found in TV shows, comics and books as well.