Extra Lancer is simply Vlad from an Alternate UniverseYou can summon Heroic Spirits from any point in time—why not from a different timeline? Besides, EMIYA probably won't exist in the main timeline given the events of stay night. The two Vlads are simply from different timelines.
Shirou Kotomine wants to capture Jeanne DŽarcThink about it. HeŽs a Kotomine and what kind of Christian wouldnŽt want to meet a real saint, much less capture her? ThereŽs no doubt he has some kind of Evil Plan involving Jeanne.
Shirou Kotomine is a version of Shirou as raised by KireiThe clue to this is in Shirou's last name. Which means that Shirou was raised by a complete sociopath, and was in turn given a skewed moral compass.
Mordred is actually Mordred AlterShe's the clone of Saber. Saber has an ahoge, except when she's Saber Alter. What's to keep the same for being true of Mordred? The question now is what exactly she's like when she DOES have her ahoge.
The Homunculus will sacrifice himself to resummon Siegfried to be Fiore's servant when it looks like the Red Team is about to win.Cause Dammit, Karna vs Siegfried round two must happen!
There are Ruler-class Servants also in the canonical Grail War, they just got dispatched before we met themTokisada's presence as the Ruler of the Third War means they were present even before the Grail got stolen, at least in the Third War, and that they were most probably Catholic Saints, even if not necessarily canonical, and that they were kept secret for security reasons. But why didn't we meet them in Fate/Zero and Fate/stay night? Because they pissed off Gilgamesh: the Fourth's Ruler declared that Gilgamesh, having ruled Earth right before The Great Flood, was evil, and pestered him until Gil had enough and killed him, while the Fifth's Ruler discovered what was under Fuyuki's Church and was killed by Gil when he confronted Kirei about it.