1) On Publish Online, when I select Privatize living people, I had some people show up that were living. I realized that I had inadvertantly unchecked the Living box on those people. If you find that to be the case you can reset them manually or use the Tools, Set Living..., which will reset the flags. You have to decide what logic you want to use for that, based on having death date only or also if birth was before a certain year roots web allows no earlier than 1930, but you may want to go 90 or 100 years back to be safe. There are tips in the forums on how to use this. If you have manually set a lot of people, you may not want to use this feature as it will reset them.
2) When you choose a person from the web page and it takes you to that persons page, it should reset your view to the top of the page, rather than being left at the bottom.
4) I have a 23" monitor on Win7 using IE9 and the margin extends beyond the screen as others have mentioned, but this particularly a problem in the Notes and Index when the scroll bar is off the page and it's not obvious how to see the rest of the information.
5) Tip that might work for those that want to add a link to their main branches, is after you publish you can copy those links and then add them to your Home page links the next time you publish. Unfortunately since the online doesn't use the db record #, it may not always be the same each time. Otherwise I find it hard for people to go many pages down in the index to get where they want to go. Might be nice to have a Link section to key individuals, where you could let us choose individuals from the index to include in that section. When published you would change the link to point to the published webpage. The other way to solve that would be if there was a search feature like on Rootsweb, which could take you to an individual much faster.
6) When managing the Account, there is no Ok button when undone, seems strange to just cancel the screen. Also it's confusing that when you choose delete from there it only deletes the online directory and not the local directory. As others mentions when you go to publish it says its still there. You may just want to clarify that you are deleting only the online version.
7) Would be nice if the Pedigree Chart started with the Root person, otherwise I am not sure there is a reason to include it on the Home menu, you really need to go through the index and find the person first.
8) When you see the "Your Information Has Been Uploaded" screen, it would be nice if the link to your new site was a hyperlink or something you could copy, would save people errors manually retyping it.
9) When using "Check site status" it's not obvious that the Processing (%) is a static number and that you need to click OK and check again. Maybe there could be a Recheck button, next to OK, so you don't have to close and rerun.
Great first effort, but until you solve the privacy issue I can't use the web feature the way I would like.