1

There used to be many, even more than (there) are today.

There were many, even more than (there) are today.

Is there optional is both sentences?

2

This Wiki article provides a good summary of the main types of ellipsis. As you can see, it does not include any type of ellipsis that would permit the omission of just the introducing adverb there.

You can, however, omit there are from both sentences.

There used to be many, even more than today.
There were many, even more than today.

We could explain this in two ways. First, they could be examples of ellipsis- comparative deletion of there are. For comparative deletion, we don't have to have an exact match between the verbs in the two clauses, so there are can match both there were and also there used to be.

There is also a non-ellipsis explanation. than can function as a conjunction or as a preposition. In the original sentences, than was a conjunction followed by the clause there are today. In the shorter versions, than is a preposition, with today acting as a noun.

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