So you've got a SharePoint site laid out the way you want it, with the web parts configured to show the custom views you've chosen, and the chrome configured to display no toolbar or just a summary toolbar. When you create a template from this site and then create a new site from that template, your web part configurations are lost - the web parts revert to a default view and full toolbar.
The list view issue has been identified by MS, but no workaround is given. Apparently a hotfix is on the way:
The chrome issue may be able to be handled by tweaking the onet.xml file to change the ChromeType attribute in the zone; I have not yet experimented with this but read about it here:
I'd love to hear of any workarounds for these issues - meanwhile I'll have to content myself by doling out a fish slap.