I think this trope is too problematic when applied this work. While there are clear cases of lots of bullets and no hits, we aren't talking about a consistent fictional world: during the gun battles we are intended to believe that the laws of nature are being messed with at the same time.

• Imperial Stormtrooper Marksmanship Academy: Justified with the mooks due to everyone having the ability to bend the laws of physics, but you have to wonder how the hell the Agents miss so often.
  • Actually the Agents are pretty accurate with their guns most of the time, with a couple of notable exceptions. The strongest example for their bad aim would be the backwards bullet dodge which Trinity does in Reloaded, the agent is firing a pistol at close range but his aim is very pitiful. Most of the other times, the agents are chasing moving targets, such as when Neo runs through the apartment blocks in the first film.
  • Considering that in the Matrix everything is in flux and everyone is fucking around with the source code, it's justified. Very justified. Justified with prejudice, in fact. ... Yes.

This is a contentious assertion: it would help a lot if the OP had said which plotlines had run aground and how. I think the additions are correct: what we see is more a case of hanging fire while waiting for the third movie. Do we have a trope for Mid Trilogy Syndome?

• Now What: By the middle of Reloaded, it's clear the authors have painted themselves into something of a corner.
  • Again, Your Milage May Vary. There are some people who think the trilogy is reasonably well planned and thought out, some think that the script is a gold-embossed version of the Dead Sea Scrolls, and some think that after the first movie the Wachowskis all got very high and fucked over the entire franchise. People have written essays about how good or badly written the trilogy is.
    • Essays? Quick search on Amazon shows at least seven non-fiction books with analysis of the Trilogy.
  • The problem is more one of pacing, which is where the rumors that the second two movies were meant to be one long movie come from; there's simply a lot of filler. One illegal downloadable copy of the movies actually re-cuts the second two down into that one long movie with a shorter total running time, and many viewers who adamantly hate the movies think it's genius in this form.

I do not think this is true enough to list:

• Expy: Maybe not intentional, but Trinity is for all practical purposes Molly.

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My comparsion would be:

Molly

• A dyed-in-the-wool crook.
• No high-minded ideals whatsover: a pure street-kid at heart.
• Stylish tough character in a Cyberpunk work.

Trinity

• Ready to fight and die for a higher cause. Cares about people.
• Not in it for material gain.
• Stylish tough character in a Cyberpunk work.

Not enough for an expy: they might both be tough, stylish, female and in a cyberpunk work but there are lots of other characters in The Matrix which fit the bill. In the Sprawl Trilogy, too, for that matter.

Morpheus is not The Obi Wan since he does not die. It is a pity the trope is quite clear about this because otherwise he fits perfectly.

• The Obi Wan: Morpheus

Crowning Moment Of Awesome: It has been argued that this series consists entirely of one Crowning Moment after another. The Wachowskis themselves get one for the special cinematic that plays before the final fight in Path of Neo. Crowning Moment Of Heartwarming: Neo saving Trinity in the end of the second movie. Crowning Music Of Awesome: The two songs playing during the credits of the first movie are Wake Up by Rage Against The Machine, and Rock is Dead by Marilyn Manson. Oh Hell yes. Add to that Neodämmerung and Navras from the third movie. Hearing the opening of either song is enough to cause extreme pants-wetting. Don't forget the Burly Brawl.

Look, a Glitch in Matrix.

Pun Based Title: Animatrics are animated storyboards.

Removed this comment for the simple reason that it doesn't work. The whole point of the "well, not exactly" line is that Smith's virus-like nature is completely different from what has happened before.

• It was implied from Smith that the other Ones created similar threats during the past five cycles (Smith, when talking to what is revealed to be another Smith, states that "everything is happening exactly as it had before", to which the newly viewed Smith clone says "well, not exactly.")