Hello,
So I do not think the basic data structure is the problem, unless mysql hotcopy does something really strange like inserting a timestamp or other changing data info every few KB in the output stream.
No, really, mysqlhotcopy performs just a raw file system copy of /var/lib/mysql taken from the locked database. If nothing particular happens meanwhile in the running database, the copy is 1:1 with the original. Easy to check with any smaller database.
I would suggest trying a tool like xdelta (on the same machine) against two consecutive backup files, just to see if it can extract similarities. If xdelta can find significant matched data, rsync should be able to as well.
I'd love to do that but I can't make it actually working:
xdelta: open ../mantis_game_20090707/mantis_bug_file_table.MYD failed: Value too large for defined data type

Same for dumps. I think it's running out of memory just like diff does with files that large, isn't it?

Also, is the transfer CPU bound or network bound? Can you send the output of rsync with the --stats and -v options?
I'm pretty sure it's the network. The rsync jobs on both machines use no more than 30-50% of the CPU. I may be wrong - please find the log attached.
Perhaps I am memory bound, could it be?

Regards,
nosek
$ rsync -kavzO --del --stats --block-size=32768 --delete-excluded \
        --exclude=phpThumb/cache \
        --exclude=glpi.techland.pl/files/_cache \
        --exclude=glpi.techland.pl/files/_sessions \
        --exclude=moinmoin/data/cache \
        --exclude=tmp/cgisess \
        --exclude=*.old --exclude=*_old \
        kno...@mantis.techland.pl:/ftp2/backup/mysql-mirror 
/home/nosek/rsync-test2/ftp2 2>&1 \
        | tee -a /home/nosek/rsync-test2/ftp2/mysql-mirror.log
receiving incremental file list
# ...27 entries of some smaller databases here...
mysql-mirror/mantis_game/mantis_bug_file_table.MYD
mysql-mirror/mantis_game/mantis_bug_file_table.MYI
mysql-mirror/mantis_game/mantis_bug_history_table.MYD
mysql-mirror/mantis_game/mantis_bug_history_table.MYI
mysql-mirror/mantis_game/mantis_bug_monitor_table.MYD
mysql-mirror/mantis_game/mantis_bug_monitor_table.MYI
mysql-mirror/mantis_game/mantis_bug_relationship_table.MYD
mysql-mirror/mantis_game/mantis_bug_relationship_table.MYI
mysql-mirror/mantis_game/mantis_bug_table.MYD
mysql-mirror/mantis_game/mantis_bug_table.MYI
mysql-mirror/mantis_game/mantis_bug_text_table.MYD
mysql-mirror/mantis_game/mantis_bug_text_table.MYI
mysql-mirror/mantis_game/mantis_bugnote_table.MYD
mysql-mirror/mantis_game/mantis_bugnote_table.MYI
mysql-mirror/mantis_game/mantis_bugnote_text_table.MYD
mysql-mirror/mantis_game/mantis_bugnote_text_table.MYI
mysql-mirror/mantis_game/mantis_custom_field_string_table.MYD
mysql-mirror/mantis_game/mantis_custom_field_string_table.MYI
mysql-mirror/mantis_game/mantis_email_table.MYD
mysql-mirror/mantis_game/mantis_email_table.MYI
mysql-mirror/mantis_game/mantis_filters_table.MYD
mysql-mirror/mantis_game/mantis_filters_table.MYI
mysql-mirror/mantis_game/mantis_project_version_table.MYD
mysql-mirror/mantis_game/mantis_project_version_table.MYI
mysql-mirror/mantis_game/mantis_tokens_table.MYD
mysql-mirror/mantis_game/mantis_tokens_table.MYI
mysql-mirror/mantis_game/mantis_user_table.MYD
mysql-mirror/mantis_game/mantis_user_table.MYI
# ... 32 entries of some smaller databases here ...

Number of files: 1617
Number of files transferred: 87
Total file size: 18029881002 bytes
Total transferred file size: 18013399877 bytes
Literal data: 123736377 bytes
Matched data: 17889663500 bytes
File list size: 43382
File list generation time: 0.020 seconds
File list transfer time: 0.000 seconds
Total bytes sent: 4361279
Total bytes received: 103628292

sent 4361279 bytes  received 103628292 bytes  31406.01 bytes/sec
total size is 18029881002  speedup is 166.96
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