I personally feel that Legends did not need to be removed. There was plenty of room in between Vlad's rise to the Vampire king Dracula (1462 as mentioned in the 1992 movie adaption) and his assassination in 1472. Legends could easily fit in there with Sonia being the one to assassinate him. And since CV III originally took place in 1492 (20 years later) it would have been enough time for Trevor Belmont to be born, grow to maturity and hunt down Dracula when he began his war on humanity. But then IGA messed it up with CoD taking place three years after 1476. CoD I feel should not have been made.
Except Legends tampered with the timeline implying Trevor was Alucard's son. I didn't think this was an issue, but after LOI konami made it clear that the Belmonts swore an oath to 'hunt the night' which if they were part of its offspring wouldn't really make sense. Also Iga retconned Legends basically accepted that after Trevor was the first Belmont to defeat Dracula.
COD was an incomplete resurrection, Isaac was the failed host/ body.
I personally find 1094 to be in error in terms of the LoI back story. It says that Leon and Mathias were warriors in the crusades yet the Crusades did not start until 1095 (one year later) So Leon and Mathias could not be in that war. We also have the fact that Mathias later becomes Dracula, yet according the Bram Stoker's Dracula (which was made canon into the CV series long before LoI) Vlad is Dracula and he did not become Dracula until (again) 1462. Both Vlad and Mathias are to totally different people. Personality, style, looks (Mathias is a pretty boy while Vlad is reported as being somewhat ugly in looks by Turkish standards). And their general attitude towards people (Mathias is very cold and removed while Vlad is very temperamental and extreme. Ergo they cannot be the same person, but IGA went and did his own thing without thinking everything through. He's a perfectionist yet he made all these errors. No that in itself is a contradiction.
The Novel never fit in perfectly with Castlevania, the series also states that John Morris saw his father Quincy die, and he'd have to be like two years old witnessing the last scene of the book, which isn't possible.
The point of LOI's ending is that Mathias escapes and starts creating his army of Darkness up to the events of CVIII.
The novel Dracula actually states that he sought the Turks who dabbled in the black arts over the [Carpathian] Mountains, it never says when. Black arts could be construed as Alchemy; the Crimson and Ebony Stones - Mathias finding the Crimson Stone.
Concerning the Mathias-Vlad-Dracula connection:
Now, the Symphony of the Night manual states that Dracula is estimated to be 800 years old. The Castlevania Adventure manual also states that before Dracula was Dracula, he was an ancient evil sorceror that made a pact with an evil deity and conducted taboo rituals in his castle every night. This is most likely the main reason why Mathias and the events of Lament of Innocence exist; to give credence to the few details concerning Dracula's age & origin as revealed in those manuals.
Agreed, and as above the novel references the Black Arts which potentially means a Myriad of things i.e. How Mathias becomes Dracula in LOI.