The "Simon Belmont" in this series is not the "real" Simon.
When "Princess Lana"note was recruiting other warriors/heroes to help her against Mother Brain, this person, who likely only has a loose connection to the Belmont family somehow managed to take the "real" Simon's place and pass himself off as Simon Belmont. After all, a guy like him is more than willing to take the credit for someone else's work. That said, on several episodes, he has been shown to have the skills and talent; nothing fake about that. Furthermore other episodes have shown him to be a good person deep down. As for how this all happened. That's another story...- Then where was the real Simon when Castlevania called for help in Simon the Ape Man? And why did none of the people realize he was a phony in Metroid Sweet Metroid?
- Her being Samus is jossed, considering how the two were separate characters in the comics. She could still be Palutena, though.
The behavior of both Simon and Alucard in this series is the result of Dracula's meddling.
At some point, Drac got a spellcaster of some sort to curse Simon (limiting his effectiveness and drastically changing his personality) and brainwash Alucard into becoming loyal to him (with the unfortunate side-effect of turning him into a Totally Radical stereotype). All the villains are the result of Dr. Wily's experiments in artificial intelligence.
From the least successful experiments to the most successful: King Hippo is an ordinary boxer who Wily captured for experiments that were intended to make him smarter. The procedures actually lowered his intelligence, and had further adverse effects that turned his skin blue. The Eggplant Wizard is an ordinary eggplant modified to be intelligent; he may not seem that bright, but then he's smarter than an ordinary eggplant. He was successful in creating Mother Brain, an artificial brain that would help Wily Take Over the World. The "Dr. Wily" that we see is Actually A Doom Bot who is there to make Mother Brain think that she is in control and Dr. Wily works for her rather than the other way around. And as for Kevin: Dr. Wily is the one who summoned him to Videoland because Dr. Wily sees him as an intelligence from outside that dimension, who can understand Videoland's scientific laws in a way that the ordinary residents of Videoland (including Wily himself) can't comprehend. Dr. Wily doesn't mind that Kevin fights on Princess Lana's side, because if Mother Brain were ever destroyed, he would be able to form an alliance with Kevin and be a member of her Palace of Power's court.- That would explain why she let Wily take control of the three sacred treasures. Or why he wasn’t around in every Mother Brain appearance.
There is a VERY good reason why Samus doesn't appear in this series.
Back when The Super Mario Bros. Super Show! was going to be "The Super Mario Bros. Power Hour", there were plans for a short based on Metroid. However, it would have portrayed Samus as being a man despite what the original game otherwise reveals. However, DIC cancelled these plans. The reason Samus doesn't appear in this show is because that would have meant having the show feature their planned male version, which they knew they couldn't after they (likely) found out who Samus really is.note 