1) I've not had this problem with contacts because I don't have any that don't have a name but I have had one contact issue. The google maps app, when searching for an address, has the contact option. when I click it I get no contacts at all even though my contacts app has many.
2) Browser Notification: I've noticed this as well. I think it's probably due to screen space that they did this. I do hope they update it to allow the notification bar at least.
3) I noticed this one as well. It also happens in handcent if you replace the messages app. It may be by design.
4) I can't really say I've had much issue with the browser. I've seen the message you talk about and I'm not sure what it means. It may be the browser logging into your google account.
5) Minor - I preferred the Droid's habit of opening a webpage in "overview" mode, where you see the whole page.
I agree with this. I've seen this issue brought up in a few reviews as well. I think this is an HTC specific browser thing since they own the browser. They may change it in the future but there is no option I know of to change it now.
#6 - My flip clock/weather updates automatically. It's not as often as applications. I've been looking at the "best practices" that google puts out on widgets and updates and they don't recommend that they update as often as applications do to save battery life. I'd guess they have the clock app set to update every minute and the weather to update every 30 minutes or so but that's a guess. This is an HTC widget and not a standard android one. Check the android market for Beautiful Widgets. They have recreated a lot of the HTC widgets and may offer more options for control then HTC has. I've not tested them as I have the HTC ones so I can't say for sure if they have more options or not. Might have better luck emailing their authors though.
7) I can't really comment on the calendar one, I've not really used it much.
8) Technically this is an HTC phone and not really a google phone. HTC has replaced a lot of the "google" experience. I'd say you get more of the "google" experience on the droid then the eris. A lot of people like the HTC Sense UI a lot more then the standard android "home". So basically in some cases you will see some of the google apps less integrated with the new ui because of this.