How to make pages/word documents open in preview first

The same things happens to me. After some digging around I found this from Apple:

Important: You cannot download a document from icloud.com to your Mac or Windows computer until the document has been opened on an iOS device.

My guess is that this is a symptom of iCloud's "work in progress" status, and that this functionality will eventually be there. Considering that you are only asking to download the exact same file that you uploaded, though, it is a pretty silly restriction.

Update:

For me, the behavior has recently changed. Now if you upload a file from your computer to icloud.com, you can download the original file to any computer from icloud.com. You still must download the document to an iOS device before you can download the file as a PDF or other format.

Yes, this can be achieved solely with Preview.

1. Show page thumbnails by clicking Thumbnails from the View Menu.

   

2. Show the Edit toolbar, and choose the Rectangular Selection tool.

   

3. Select the rectangle that you want to crop each page to.

4. Select (⌘-click) all the pages that you want to crop in the page thumbnails.

   The pages don't have to be sequential, and you can select all pages with ⌘A.

5. Click Crop in the toolbar.