Thanks for your post.
I'm afraid we don't offer any pre-filtering in SQL Compare because of the way we need to register the whole schema to understand all the object dependencies.
However, you have not been the first person to suggest the idea, so I've added you as another vote for SC-2471.
You might like to also suggest the idea on our uservoice
site as this is a bit more visible and other users can vote on the idea too.
You may also like to vote for the suggestion to make SQL Compare 64bit
, as this would probably help with the memory issues you're finding.