As a stand alone movie, unsure of its success, Barnabas's origins is the best starting point. It has a perfect beginning, middle and end. It's tragic, it's gothic, it's horror filled...it's pretty much everything. It's epic. And with Burton on board as director, I think he could rock a period film (loved Sleepy Hollow).
I would definitely choose the 1700s as the starting point.
Barnabas being unchained from the coffin can start 1897 and the audience would care because it would be seen through Barnabas's eyes (the lead character). Naturally, he would go to meet the current family once he was freed, just like he did when Willie freed him. He and Quentin could start off as sort of enemies and end up as relunctant allies. To tie things in with the first film, Angelique could certainly be included, just like she was in the original.
I think it would flow pretty naturally.
And then for whatever reason, Barnabas and Quentin go their separate ways, maybe Barnabas is chained in the coffin again, or maybe he isn't (I think it might be more interesting if he isn't). Then a third film picks up in the present with Elizabeth, Roger, Victoria, Carolyn, etc... Willie can definitely be in there somewhere..... Maybe the family is in danger and Barnabas and Quentin have to come together again to stop whatever evil haunts them.