I would like to be able to pass HTML entities to Template Tags that take query-string-style parameters. I think the easiest way to do this is by putting parameters with HTML entities in quotes, although it may also be possible to "escape" ampersands in entities by preceding them with a backslash or something similar.
Alternatively, do NOT deprecate the equivalent PHP function-style tags. I've personally run into problems with wp_get_archives versus get_archives, although there are probably other examples.