allow me to answers some of the 'plotholes'.
1. The reason why the Vampire Killer was the most powerful weapon in the trilogy (and the only weapon capable of killing a true immortal like Dracula) is beacuse the weapons was forged from one of the nails that was used to crucify Jesus, says so right in the travelbook oin the first game. So essentially it would make sense that the VK is the ultimate symbol of god and everything holy, it had the blood of said god/jesus assmiliatted into it (sorta) therefor his/her/its power as well, the upgrades just made it better.
2. The Toy Maker was 'woken up' by Dracula in the past for some assistance (shits&giggles) in creating more creatures for the castle (the puppets, the resurrected Daemon Lord, etc) and other things (the Electric Batteries Trevor finds and makes use as secondary weapons) while the Toy Maker didn't really come back (due to his heart still in hiding amongst his puppets) Dracula may have let the castle blood animate him for the Vampire Lords benefit (his corrupted appearance in Mirror of Fate. this would also lead to how the old man recognizes the Prince after regaining his memories, he would see what Dracula had him do while under the influence of the blood/curse) maybe his disappearance afterword would be that he was taken to heaven.
3. Carmilla, the secuctive witch/vampire queen. while she was killed off for good in the first game, Inner-Dracula, in the blood form, didn't want the only thing keeping it alive leaving the castle, so it tried a different approach at first with making a doppelganger of one the few woman that could have an effect on the Prince of Darkness (besides Marie since she was protected by god to help her husband, and possibly Laura, though she is gone) so it created the twisted clone of the late Queen based of the time she lived in said castle (the thing was around since the Bernhards, since they summoned it, and was bound to the castle in a form of sentience. So it would obviously know of who and what has been going on from its arrival to defeat at the hands of the one who's power kept it alive)+ add the knowledge of how the two initially met and what it knew of Carmilla (she had a slight attraction to Gabriel in the first game as well as her human appearance) and ramp that up to yandare qualities and you got yourself a twisted copy of the original.
4. The 'shield' on Alucards hip isn't really much of an effective itm to use as a shield, i think it was more of a place to store items (like Gabriel's pouch for Dark Crystals in the first game)+ it also helped holster Alucard's sword (The Crissaegrim) when he was still using the sheathe for it.
5. Marie coming back in LoS2 was god's way of steering Dracula away from his monstorous habits, helping Alucard and Marie in his/she/it's own way. he/she/it may have had a hand in Gabriel becoming Dracula (as he was the only one who could stop Satan (to the point that Satan was terrified of the prospect of going head to head against the Vampire Lord with god-like powers) but the god didn't want to go down and risk being killed by a pissed off Dracula (with its own power, the Vampire Killer). back to the point, once Marie did her part in helping her husband, she was taken back to heaven (not really sure why, as i'm sure she wanted to be there for her husband and son) this just makes me wish for a epic family reunion including Victor, Simon Sypha Marie and the two vampires.
6. The only 'past' segment of the game, where you legitimatly were in midevil times after Mirror of Fate was essentially the prologue only (the meeting between father and son just showed what happened after the Great Explosion and leading to Dracula disappearance along with the castle vanishing. all the other segments where you went back to the castle took place in a seperate dimension (possibly the same dimansion where Gabriel struck down the Forgotten One) that was outside of the boundries of time and space but connected in several areas that aloowed Dracula to go back and forth between the two settings (Modern Times and the Castle).
7. The way Alucard knew of Satan and Zobek was through the mirro on the night he died, as he lay there dying, he saw what really happened to his dad and how he became Dracula. After the events of Mirror of Fate, durin the time from then till their meeting Alucard would eventually formulate a plan to get back at the Lord of the Dead and the Fallen Angel for what they did to the family. to an end hissword also played a special part. Also the Mirror of Fate was sentient in a way, as stated by young Trevor/ the Lost Soul being part of it. Alucard also would have tracked and studied the Acolytes from afar to find out how they woul play a role in Satan's return later on, something he would end up informing his father on.
8. Zobek needed a bodyguard as he was stripped of all his power right after his first death (at Satan's hands) and woke up in the realm of the dead (Limbo?) so he obsessivly researched and tried to recollect his power to come back to the mortal realm (which worked later, as seen in LoS2). so he created his bodyguard as a means for protection, seeing as he knew of the acolytes. he also collected the Vampire Killer as a way of getting Dracula to help him stop Satan and his children by making a deal he knew Dracula seemingly couldn't refuse (didn't work out for the Lord of the Dead though). however, Alucard also noticed this and would inform his old man of the wherabouts of his old weapon.
9. Victor's combat cross is most likely the same on that Simon used during his confrontation with his gramps (which was orifginally Trevor's). it would have been heavily modified like the Seraph Shoulders, Dark Gauntlet and Cyclone Boots that Victor also had on him. The devil mask was most likely left where it was, Zobek retrieved it , or it was sucked into hell for unknown reasons.
10. Alucard most likely stopped using the Dark Pain, seeing as it reminded him of his former life as a human, wasn't as effective as the Crissaegrim, or has it stored away in his poct dimension.
That's all i answered for now, feel free to contribute.