1. Is this what you have in mind: https://gist.github.com/marcus-nl/7ba3d360ad399d07d431 ? (I'd move the "hibernate.schema.*.filter" constants to AvailableSettings)
Note that I used seperate configuration properties for create, drop and migrate, since that is needed for my usecase at least.

2. Sequence was indeed an oversight. However, my thoughts on index and unique/foreign keys were that if you create or drop a table, you'd (usually) want to do the same with those associated objects. I can imagine there are cases were that is not the case though. Let me know if you want me to add these filters (in addition to Sequence):
(a) Index
(b) UniqueKey
(c) ForeignKey
(d) AuxiliaryDatabaseObject (applies to create and drop, not migrate)
(e) InitCommand (create only)