Actually, it is believed by many that those sequels weren't actually made. At least, not really made by the Wachowski Brothers.
Larry Wachowski was married to his wife Thea for about eight years; then, after The Matrix came out, his behavior abruptly changed. He descended into the sexual underbelly of LA, first as a fanatical new devotee to BDSM, and, later, as a transvestite and then (it is rumored) as a full-blown transsexual. Comments made concerning an earlier film, Bound, would seem to imply that this was a long-term preoccupation of Larry's and, indeed, is treated as such by many fans.
However, the truth is a bit stranger. Ilsa Strix, the woman who is generally acknowledged to have introduced Larry to BDSM, actually was a relative latecomer to his BDSM phase and was primarily a love interest, not a guide. What she did introduce him to was intramuscularly-injected ketamine.
Ketamine is widely known as a "party drug," generally as a poor substitute for ecstasy. But ketamine is neither a stimulant nor a psychedelic, strictly speaking; it is a dissociative anaesthetic, far more similar to dextromethorphan hydrobromide (DXM, in 'Tussin) and PCP than to ecstasy, mushrooms, LSD, et cetera. As "party drug" people are usually wary of needles, they tend to snort ketamine. People tending to enjoy more, ah, intense drug experiences may inject it into a muscle.
Ketamine, injected into muscle, triggers an extremely intense dreamlike state that lasts for days (according to the injectee) or ten minutes (according to consensual reality). The injectee is otherwise unconscious during this time.
It is believed that Ilsa Strix (professional Dominatrix, ex-wife of Buck Angel, for whom you probably do not want to do a Google Image Search) introduced Larry Wachowski to an experiment she had conceived of while watching the film Altered States; what if ketamine intoxication could be combined with the endorphin and psychological rushes resulting from painful domination and sex? A typical session consisted of a long period (sometimes hours) of degradation, beatings and "confusion play" at the hands of Buck Angel, followed by prolonged whipping and prolonged orgasm denial, and then a sudden injection of ketamine at orgasm.
As one might imagine, this had a hell of an effect.
What no one could predict was the immense amount of power that Ilsa Strix would thereafter exercise over Larry Wachowski and, thus, the Wachowski Brothers as a pair. As Larry became more and more fixated on Ilsa and her play, she began transitioning their private relationship into a more public role. Private humiliation turned into public humiliation, with the tall, formerly burly Wachowski forced into increasingly effeminate costumes for degrading public display.
It is thought that, at this time, Ilsa Strix guided the drug-addled, traumatized Larry Wachowski to alter the Matrix epic (originally intended to be an HBO original series, with a theatrical pilot) into a trilogy with the second and third films shot simultaneously á la Back to the Future. Andy Wachowski, who had been in favor of keeping the series theatrical (although he disliked the confinements of the trilogy format) saw a theatrical trilogy as a valid compromise.
The storyline that the brothers had thought out was greatly compressed, and Ilsa Strix's ideas were added (the Twins and the Zion Orgy thing, for instance, but also the recommendation of the incomparable Monica Bellucci). Much of the ambiguity of the first film was discarded and a more conventional Christ mythology was adopted; it is believed that the obvious archetypal interactions of the first film were what Neo was truly trying to destroy -- essentially freeing humanity's minds so that its asses would follow.
In short, the Wachowski Brothers originally intended to present The Matrix series as an allegory of mankind overcoming its genetic predispositions to certain shared narratives (monomyths) that Larry and Andy considered harmful. Instead, the trilogy ended up as just another exercise of those monomyths.
Whatever the outcome of that experiment, the Wachowski Brothers have since shown no signs of fulfilling their early promise. The affair is rumored to have greatly weakened the brothers' abilities to work together, and their "collaborations" since have essentially been for show, more akin to McCartney and Lennon's "collaborations" than a truly shared affair.
TL;DR: Ilsa Strix essentially made #2 and #3.
