I have been readying the next version of PHPTemplate for the 4.6 release (the RC should be out very soon now). You can get this in CVS now, but it is NOT meant for 4.5. I am still undecided wether to back port it.

1. Did away with the template caching. I did some benchmarking and it appears that file_exists() is nowhere near as heavy an overhead as I thought. This means you don't have to go to admin/themes to have the cache refresh.
2. $seqid and $zebra variables are now available to all templates without needing to do the template.php hack (see: http://drupal.org/node/16383).
3. $node object available in page.tpl.php on node view pages. This allows for some very creative layouts, and styling the entire page different for different node types (by adding a node-$node->type class to the body for instance).
4. Automatic loading of node-$type.tpl.php files. You can create different templates for story / blog / etc. nodes. Practically, I still think CSS would be better for this, but it has been requested often, so here it is.
5. Automatically uses a favicon.ico if found in the theme directory.

Unfortunately, the link configuration is still less than ideal. I am looking into a possible solution for that, but most methods actually involve breaking compatibility with xtemplate and by extension Drupal core.