I think a cron job should be setup to optimize database tables every week. The first time I did the database shrink to half of the size. Nowadays, I usually run PhpMyAdmin option to optimize every table every three or four days. Usually, it becomes 20% smaller....
I don't know if it is a problem related only to my webhost provider configurations, so if you could try it, and post the results, we could determine if there is indeed a general problem or I have something misconfigured...
have noticed that my cron.php script on my site can take quite some time; up to minutes and some cpu cycles.
now i was thinking, if i would wget the cron.php's on these known drupal sites, i will make it harder on these sites and harder on drupal.org as well, since these sites will update drupal.org pages as well.