1) How can I download ONLY new/unread items and no read items
2) How can I see only NEW items
In this release I have tried to address them.
1) If you want your periodic downloads to only download the new items, then the way to do it is NOT to choose any favorite tags or any favorite feeds. With no favorite feeds/tags, ReaderScope will query Google reader for a generic list of new items in your reading list. This will get you only the new items. This was possible already; but there was a problem to access these only new items.
The first screen of ReaderScope is designed to give you a summary of all your Google Reader feeds. So it will show you all the feeds and all the unread counts irrespective of they are downloaded in the cache or not. So you couldn't tell which feeds have cached items. In v1.1.2, the feeds that have at least one cached item will be marked brighter than the rest. So now you can see which feeds have items downloaded from the last periodic download.

2) Some users prefer to only read the latest downloaded news. For them the new unread items are now highlighted. As before, the read items will appear in dull colors. The unread items will appear in white color and the unread items that are less than 24hr old are shown in bold white letters.

Let me know if this works for you.
For those who found the filter button introduced in last release useful; here is a good news. If you want to hide read items permanently, then go to Settings->Miscellaneous. Check "Remember filter state for read items". Now if you turn the filter ON to hide the read items, it will remain so until you explicitly turn it OFF.

For those who read news by labels, it becomes confusing to tell which feed the news came from. That problem is addressed in v1.1.2 too.

(Now I won't mistake news from my Onion feed for genuine news ;) )
Thanks for the error reports. I am working on them.
Let me know if this version fits your needs.