Not that anyone seems to care about file sizes except for me, I believe that OCR PDFs are larger than regular PDFs which would expand the II folder more quickly. File size remains an issue for those of us who want to do off site backup using a (slowwwww) DSL connection.
I'm sorry but that's not true. Acrobat uses an algorithm which is obviously secret, but it actually reduces the file size. For instance I just had a PDF document that 5.5 MB, I OCR'd it and now it's 3MB. So that's not really valid. Think of it this way a full page picture can be a few MB. A full page of text is 1KB. I don't know the exact workings of its algorithm. But you can even optimize for web publishing which really shrinks it down to almost nothing.
As to your backups, you should just not include II in your offsite backup ENC file. Let that be backed up by a third party application like Jungle Disk or CrashPlan. Those do incremental backups so you're not wasting time uploading the same stuff over and over again. II are not part of the database. (Even the SQL database can be incremental, but AC refuses to release the SQL SA password.) For now just make the II incremental. I could be uploading a few MB a day, but since they won't tell me the password, I have to upload my full database everyday. I do keep II incremental because like you my connection is slow and I had to adapt.