Well it would appear the the Jury is in and a number of people think the default Theme used for Thunderbird is actually ugly, or just plain difficult on their Windows setup. Note that I said windows. It is the Aero theme that has got people shaking their heads.
There is a fairly simple solution however.
Change to a non default Theme.
The Thunderbird Theme web site lists 81 current themes, I would assume with that sort of number of Themes one of them would suit most people.
If it is just the transparency that is the issue, then the no glass theme may be what you want, or even the no Aero
Here are a couple of standouts that appeal to me for various reasons, they might appeal to you as well.
Classic Toolbar Icons for WinXP
Outlook 2003 BlueTB
Silver Skin (for Thunderbird)