After analyzing a few cases where the plugin was failing I decided to release a candidate version for the plugin. Everything has been fully tested again (though still could be some minor issues).
The log system has been notably improved and for every digest a new register is added to Subscriptions>Sent Emails Page with some details such as how many emails were sent and if one of the users did not get an email, the screen reflects the reason.
This version also fixes some detected bugs related to post types/categories and weekly/daily digests.
There's also a new column in subscribers list where you can see what post types is a user subscribed to.
Please, install this version on your system and do not hesitate to add your ideas/comments here.
Here are the updates, please, see my last posts to get the last version of the release:
UPDATE 1: Unexpected output when the plugin is activated.
UPDATE 2: Post types without any taxonomy like categories or similar were not being sent.
UPDATE 3: : Release Candidate 2