Christmas Rushed: The most likely reason that X6 failed to reach its potential. Not only did it come out just a few months after X5, but the North American version hit the stores mere days after the Japanese version! (December 4, 2001 and November 29, 2001; respectively. We all know how that turned out...)
Creator Backlash: Kenji Inafuane became apathetic to the franchise post X5, due to Capcom deciding to milk the series for all it was worth. He may have gotten over this when he tried to remake the series starting with Maverick Hunter X.
According to the Official Complete Works, Inafune himself made the decision after he finished the design for the main character, deciding people would not relate him to Mega Man because he looked too different. So he had someone else design the main character, and instead presented his design as the "side character".
X: Referred to often as "The Blue Bomber of the 22nd Century" or the far pithier "The Azure Hunter". Other times, especially by fangirls, "Ekkusu" is also used.
Zero: "The Red Ripper" or "The Crimson Hunter." An odd inversion is that his popular fan "full name," Zero Omega, turned out to have a significant connection (which you should already know) to the Sequel Series.
Gate's battle armor is sometimes referred to as the "Zero Armor" because of the source of his research. Not to be confused with Zero's own ultimate upgrades.
Screwed By The Video Game Company: Keiji Inafune apparently wanted to make more Maverick Hunter X remakes of X2 through X6 for the PSP. Unfortunately, due to apparently low sales, Capcom's executives vetoed it. What makes this worse is this is tied in with the Mega Man X Collection. The makers of the XC had developed a large series of improvements for each game (such as re-dubbing X4, giving X6 a new translation, re-mapping one of Zero's moves in X6 so that fighting on ropes was no longer extremely dangerous, and throwing in other various extras). However, someone at Capcom Japan didn't like this, thinking the extras would make the XC overshadow the upcoming Maverick Hunter X series, and so forced the XC's developers to remove all extras and improvements (which were IN the game at some point, as evidenced by a line change in X1, and the re-mapped Zero move from X6 having a different command listing, but the actual way to perform it remaining the same) so that the MHX series could lay sole claim to them. Naturally, the series died after the first game, and so the extras ended up never being used at all.
They were still in late enough that they were still referenced by info on the box and manual. The removal of the new and updated content was pretty much almost literally a last minute thing.
What Could Have Been: Maverick Hunter X is said to be Inafune's reimagined storyline for the series, with better graphics (as it's on the PSP) and focus on plot and characterization. Unfortunately, it didn't sell well.
The design for X was actually not the Mega Man-esque one we know, but instead a red robot with boob-lights and long hair we know nowadays as Zero. Because he thinks that the design doesn't look like the original Mega Man, Inafune discarded the design and then created a new character for that design. And then Inafune says thatZero will steal all the good scenes.
According to this article the person who designed X's Ultimate Armor for X4 also made an armor for Zero, that would've been related to Dr. Wily. It sadly didn't make it into the game. Though this does explain why the Black Zero code in X4 didn't do anything: like the purple recolor of X, the new color just meant that the code worked and that the secret armor was unlocked.