At the end of the day, all of the major CMS' are basically the same (php, sql, javascript/ajax, etc). All open source, db driven, very large dev communities and extension/plugin options, etc. In the right hands, they can all be "pimped" to do amazing things. For awhile they each had their schtick: WP for simplicity, Drupal for complex/flexibility, Joomla was a little of both. Nowadays, WP is no longer just a blogging tool and has become very powerful platform. Drupal has become much more user friendly. Joomla still sits in the middle (and happens to be my goto platform for clients). When explaining to clients, I often use the desktop OS triad as a parallel. WP is like Apple OS, Drupal is like Linux, Joomla is like Windows. They all can help you be more productive. The only one that is better is the one you are most comfortable using.
In regards to OP points about removing plugin comments and such to eliminate footprints for uniqueness, well. first off plugin comments are the least of the footprints Google can identify to recognize it as a WP setup. There are many other "patterns" in WP...and all standardized systems for that matter. believe me, even if there was a way to have no plugins on WP, Google could still easily recognize it.
I would wonder, outside of security reasons (which is a valid reason) why would you want make changes that could themselves be a pattern/footprint. If you were running a blog network, the last thing you would want to do is modify/optimize every install the same. To get the most "natural" setup, you would have to mimic "natural" installs. Which would mean a blend of modified/tricked out setups, moderate setups, untouched/default (the majority), etc.