There are a number of changes that can be made to the look and feel of Thunderbird Version 3.x.x that make it more like the version 2 interface.
If the large header pane on messages with the new reply button in the header is not for you. Install the Compact header add on.
Following this install you will need to customise the toolbar to put the Reply Delete etc buttons on the main Toolbar as they will disappear when the addon reduces the header to the old view. To do this right click the Toolbar, select customise and drag the buttons you want to the toolbar.
You might also want to display messages in their own window as this is what version 2 does, rather than in a new tab. Select the Options entry on the tools menu and then select Advanced and then Reading & Display. Change the entry under open now mail from a tab to a window.
Missing message count in folder view can be cured by installing the Extra Folder Columns addon.
Folder view can be changed to ALL from unified it you don't like the new unified appearance with all in-boxes clumped together. Simply select the View | Folders menu.
If all else fails and you really really want to be using the old version 2 you can download it here