forgets Zero, then conveniently remembers him?
Of course they could have made X's not remembering Zero a plot point which, at the end, might have been resolved. I mean it wasn't really necessary to retcon that, even if they felt bringing Zero back was.
Did you people even play X5 lately? X forgets Zero when Zero goes maverick. X6 goes from the Zero ending in which he is a playable character. Completely mutually exclusive events. Zero himself delivers the final blow to Sigma and X carries the saber
in his memory. X6's intro make this perfectly clear.
After that, it falls to pieces. Nightmare Zero becomes irrelevant, which was terrible writing. He's never even mentioned again, not even brought up.
The Zero Nightmare had the explicit purpose to give Isoc his excuse to start the Nightmare investigation so that he could lure out and locate the real Zero. It's a stepping stone to the next part of the plot, that is the mystery of Isoc, which requires Zero's return.
After it's defeat it's often referenced by bosses accusing Zero of the Nightmare, still. Gate on the other hand, has nothing to do with the ghost of Zero that Isoc is hunting. He also noted he could care less about even the real body of Zero. He only went along with Isoc's plans so that he could test himself against the original, and that was low on his list of priorities as he, unlike Isoc, figured Zero was dead.
Zero shows up after the Zero's Nightmare's defeat because he's been trying to clear his own name from that fake. X took care of it for him, and therefore Zero felt it was time to return. In one ending he again references the fact that he needs to take care of that and other matters before he can return to the frontlines.
All in all, you're putting unjust emphasis on one minor plot element that only serves as a stepping stone toward the rest. Taking care of it is the introduction of X6, not the main story.
You've got a whole plot ready to revolve around the real mystery of the Nightmare Virus, and instead it just becomes "oh, well this guy is insane and sent the obligatory 8 maveri-I mean, Nightmare Investigators to come get you".
The real mystery of the Nightmare was explained adequately from start to finish. It even went in depth about the origins and motivations of its creator. Tying all that to both Alia and the main characters.
I love Zero, he's what hooked me on the X series, don't get me wrong, but he simply was not necessary in X6 as a playable character.
From a gameplay perspective, Zero was wholly necessary.
From a story perspective too, his death in X5 makes absolutely no sense unless he's subsequently revived like X was. His creator is nearby, he was revived before, X was revived as well. It is the obviously sensical way to go.
From there, X6 puts Zero in the opportunity to figure out the mysteries behind his resurrection. In doing so, he stumbles upon a fake of himself, has the opportunity to ask Thomas Right and even raised his sword against the mysterious man that knows him inside out. Zero's resurrection was all about furthering the Wily storyline.
For the first one specifically, that's a mark of poor planning / creative direction. In orther words, they should have thought more deeply on what kind of game they wanted, anticipated that Wily would never return, and deliver closure.
Are you kidding me? X6 is at fault because 2 years later some different team members decided to tell the preceding plotline to screw itself? This is a GAME series, you should judge it with the well known limitations of the format, not within the idealized conditions of writing the whole as a self contained unlimited page book without deadline by one and the same writer. As such, you have it backwards, you can never blame something what its sequels failed to do unless the sequel is handled under the aforementioned ideal conditions of writing. Judge the story for what it is intended to be, not for what it isn't.
X7 completely ignores this and everything before it just to throw in Zero, a new character, the same boring Sigma fights.. Its damn near trash.
X7 does not ignore Zero's seal. In fact, X7 answers several mysteries about the reason that he sealed himself. That seal was always presented as occurring at some indefinite future time.
It wasn't in the Megaman X manual. And, that still means the game itself is badly written. Excusing the game's shoddy dialogue because the manual conveys the real idea is a pretty poor defense.
That was a different time when games were simpler. That's like expecting R1 to have the same level of storytelling as R8. Because X1 is a game of a certain genre, the story was kept to a bare minimum and told in the manual.