A couple of months ago I embarked on a mission to play through all the (non-Lords of Shadow) Castlevania games in a Timeline-based order... now by Timeline-based order, I mean that I have put all the games on a single timeline, irregardless of whether they are actually meant to be part of a single timeline or not. So it has included things like Castlevania Legends, Order of Shadows, etc, all jammed in together. I've even gone further into fan fiction territory to order things like Super Castlevania IV and Haunted Castle as being separate events to the original Castlevania (a third and fourth encounter with Dracula, to be precise) just to give me a nice order to play them in!
So, I have recently finished up CotM and have just started on Order of Ecclesia and what I find interesting playing the games in 'timeline' order is that coming from Symphony of the Night (by way of the Radio Drama) into CotM, it really does feel out of step with the rest of the series. The lack of Belmonts, the backstory of their being an encounter with Dracula 10 years earlier, the different setting... it really does make CotM not feel like part of the regular Castlevania series and timeline.
But then, once you hit OoE... it actually reaches back and makes CotM feel more like part of the timeline after all. Now we know that the Belmonts have disappeared from history, that other groups have tried (and failed) to fill the gap... even Dracula's remains in OoE are being held in some kind of coffin/statue/thing that is kind of like how Dracula was sealed in a coffin at the start of CotM.
IMO, all CotM needs to make it feel more 'in tune' with the series would be a prequel comic/manga or (better yet) game that tells the story of the 1820 sealing of Dracula, framed by the idea that the Graves and Morris Baldwin are working on a way to stop Dracula because the Belmonts have disappeared and I really think it would tie CotM in well.
Of course, it does bring up the problem that Dracula is being resurrected a lot during the 19th Century - even with the N64 games omitted, that would be 1820, 1830 (CotM), 18?? (OoE) and 1897, coming off resurrections in 1792 (RoB) and 1797 (SotN). No wonder Dracula is so cranky, his nap is constantly being interrupted!