Bulk merge creating multiple address (and email) records of same location type
The address aspect of this has recently been raised as a bug here:
https://issues.civicrm.org/jira/browse/CRM-18455

And has been patched as part of:
https://issues.civicrm.org/jira/browse/CRM-18338

As for the rest of the merging logic - where it creates many email addresses (phone numbers, and other 'location blocks') of the same type, I agree this doesn't seem desirable; but deciding which phone/email to keep isn't always straightforward. The current logic is:

When force merging if there are any conflicts the 'main' record takes precedence, otherwise any information from the 'other' record is added to it. Ie: all emails would be added. If there were two addresses of the same type then the 'main' one would stay on the record.

I also posed this question on the civicrm-dev mailing list as to whether this is the desired behavior and I've created a follow-up thread on the forum: https://forum.civicrm.org/index.php?topic=37165

Please feel free to get involved =] It would be great to improve this tool and have it working as desired - once we know what 'as desired' looks like.