1. There's no small, unobtrusive way to monitor the progress of downloads.
Actually, in OS X, the Chrome icon in the dock has a small pie chart overlay during downloads that indicates both the number of pending downloads as well as the aggregate progress of all downloads. If your dock is hidden, you can quickly and easily check the progress by hitting Cmd-Tab. In Windows 7, the "tile" in the Windows "Dock" fills from left to right, like a progress bar, to show the aggregate status of downloads. You can also click on the in-progress download, dismiss the dialog, and the file will open once the download completes.
2. The large number of options makes finding what you want hard.
As mentioned, the search feature is handy, but not always sufficient. One nice aspect that gets overlooked is that the in-tab preferences are fully addressable: you can actually link to specific pages and panels. Though this doesn't help you find a preference in the first place, it does make communicating the location of known preferences much simpler.
3. The search field covers the content of the site, if you were searching and a match was under the field, or you wanted to click a link/button under the search field, you’re out of luck.
Actually, the search field will intelligently slide out of the way to reveal matched content that it covers. If you need to click something underneath it, you can hit Escape to dismiss it, and your previously entered text will be saved and pre-filled the next time you hit Cmd-F.