Then again, Reiji, Xiaomu, KOS-MOS, T-ELOS, and M.O.M.O. didn't have amnesia when they first entered the Endless Frontier. There's a little YMMV though, since the latter three are all androids, while the first two are known for dimension hopping, and as such, probably wouldn't be affected by this kind of scenario after doing it for so long.
On that note, why no Wodan Ymir? He could have at least appeared at the penultimate level and instead of some Sanger clones, they could just use both W-15 Wodan Ymir and body snatcher W-05 Gagun Laos. Sanger's got so many clones nowadays anyway.
Too much awesome/collateral damage, considering their fight broke through something meant to withstand an alien apocalypse. Just imagine what THREE of them would do.
In chapter 23 of PXZ2 (the Balrog chapter), activating the Dragonturtle engine's Limit Break requires one to shout the passphrase "Emergency boosters, activate". Urashima specifically asks X to shout it, then asks Reiji after X's shout fails. What is this a reference to? It could be a Final Fantasy VIIActor Allusion, but that doesn't explain Reiji's involvement.
The futuristic series (Mega Man X, Mega Man Legends, Space Channel 5, Xenosaga, Strider, Captain Commando, Cyberbots, and Star Gladiator) canonically take place at various different points in the future, some even being thousands of years apart, yet these games treat them all as if they happen concurrently, since most of the characters from these series are familiar with each other.
The "present day" has some similar issues too. The settings of Shenmue and Ace Attorney are literally 30 years apart.