No, was not a mistake, but a very intentional change.
The PHP trailing ?> has been considered harmful since 2007 (see r23531 for some more details) and it is not needed in pure PHP files. (Obviously it is needed if you mix, say, HTML and PHP via something like QuickTemplate, for example.)
Since 2009, MediaWiki.org has had an AbuseFilter in place to tag edits in which users add that unnecessary closing tag. Perhaps that filter should also display a warning message?
So yes, let's not add the PHP closing tag unless it's really necessary — which, by the way, it isn't in most cases. :-)