The second two were crap but not because of plagiarism. For the record the plagiarism accusation is so demonstrably false it's got its own Snopes entry:
http://www.snopes.com/politics/business/matrix.asp
The 10 Disc "Fanboys Only" Matrix Box Set has the full analysis of why the sequels failed, the Wachowskis decided to eschew a commentary track of their own to present two by philosophers and critics. The philosophers love all the films, the critics hate the latter two but have some time for the first. The reasons for both sets of opinion are cogent and well thought through.
The critics point out that the first Matrix is revolutionary in that it asks a lot of an audience in terms of the way it plays with reality but it gives a lot in the way it presents a science fiction universe unlike any depicted before. Instead of post apocalyptic grime (which is presented as a footnote of history) or high camp glitter the future inside the Matrix is this polished, designed "game world" filled with extravagantly but stylishly dressed martial arts super heroes. Then, as the series progresses, the "real" world which resembles a hundred other post apocalyptic movies gets used more and more, the stakes become woolly, the plot focus becomes blurry and we lose the ability to care about what's happening.
The philosophers, on the other hand, go through checklisting all the philosophical concepts the movies try to convey; "try" being the operative word. The philosophers are not so keen on what they see as the "Manichean" dynamic of the first movie where good and evil are clearly and allegorically separated. It's fun, but intellectually childish. As the films progress the Wachowskis attempted to introduce more sophisticated notions of individual choice and responsibility but they can't handle fitting those into a movie about "robots vs kung fu". To be fair it's not an easy task for someone to set themselves, I'm not really surprised they failed.
It has been a source of disappointment to me since the whole series finished just how keen people were to buy in to the simple explanation that the Matrix Sequels sucked the way the Star Wars prequel trilogy sucked. They both suck, for sure; but for different reasons. The Star Wars prequels are lazy, incoherent and pompous, the Matrix Sequels are bloated, incoherent and over-ambitious. I applaud the Wachowskis for over reaching, because even today there's something to be found in the Matrix Trilogy for those willing to dig.
The Matrix Trilogy deals with more complex issues than everybody's poster film for intellectual worth of 2010 Inception. Inception is quite easy to pick apart, it just takes a little time and effort. Some of the themes of the Matrix have been central to the human condition for millennia. The worst I can say about Reloaded and Revolutions is that they are dull and incoherent if you don't have a solid grounding in the philosophy of self, fate vs. free will, the nature of reality etc. They can still be dull even if you do know what they're trying to do and you have an instinct for decent storytelling because they don't tell their story decently.
I'm not apologising for them, they're not good movies. However they're about the best bad movies that have ever been made because in their disappointing morass of uninspiring specatacle there are genuine attempts to talk about some really mind blowing stuff. No film maker before or since has attempted to make a fun, accessible movie about these concepts. The reasons they don't should be in recognition of the insane difficulty of the challenge. I suspect it's more because most people just think they're terrible movies like all other terrible movies and "probably plagiarised" to boot.
And I think that's a great shame.