I just want to point attention to this:
http://forge.mysql.com/wiki/OnlineBackup
I think that it should be investigated. We will soon (also 2 years is pretty 'soon') have a myriad of Storage Engines available with MySQL – some supporting special type of indexes that the standard engines do not support. Some optimized for certain types of data (such as GIS data for instance). And so on.
To maintain SQLyog backup tools to support all this will probably a lot of work. Probably it would be better to integrate this new API in SQLyog and SJA.