Megaman X/Megaman Legends References
Although Megaman X and Megaman Trigger are two different persons, one cannot deny some similarities between the mainline and the spin-off. For instance, Megaman X and Megaman Trigger were designed to hunt down Aberrant Units and protect the humans. While Megaman Legends 2 ends the controversy once and for all of Megaman Legends' place in the mainline Megaman Universe, however some post-Megaman Legends games tease us into thinking they are.
For instance, taking a look at Megaman X5. If you get the bad ending (let Zero go Maverick), Megaman X will mention he wants to create Elysium. Before that, X's bad ending will also feature a mysterious figure that would resemble Yuna from Megaman Legends 2. If that's not all, Megaman X5 features a plot that could be compared to the Carbon Reinitialization Program where Sigma seeks to crash something into the city, destroying an entire population. Also, Alia is a spotter for you.
Megaman X6 has a few references to Megaman Legends. It's no longer part of Keiji Inafune's line. Aside from some robots looking like the Reaverbots, we also have the explorers who can be compared to the Diggers of the Megaman Legends continuity. Gate was once a digger, Alia was once his spotter. Alia works as a spotter yet again. Also Megaman X having the Z-Saber is almost like Megaman Trigger/Volnutt getting the Zetsaber (a reference to Zero). In Megaman Legends 2, it was said that the sword belonged to a hero. It must be a reference to Zero.
Megaman X8 is also chock full of Megaman Legends references. The story features the Orbital Elevator leading to space. Doesn't that remind you of ELYSIUM in Megaman Legends 2? It talks about the new "golden age" which may refer to Elysium's creation. The Sigma Palace strongly resembles that of Elysium. Also Megaman X's final boss Lumine is a Megaman Juno/Sera hybrid who seeks to create the new age by eliminating the last age. Too bad that Megaman Legends 3 as canned.
Megaman X Command Mission sort of has a few Megaman Legends references such as digging for money. The game features Megaman X fighting against a criminal group who turns out not to be the final antagonist (and Epsilon looks like a meaner version of Teisel Bonne). Colonel Redips can be viewed as a meaner, more evil version of Megaman Juno. Both Redips and Juno were once comrades to the main characters but had their own selfish motives. Also the final battle with Redips takes place in space where some of the game's bosses have to be fought all over again.