Making content and functions maintainable in the long run
I'm not quite sure what you mean. 

Block content can be held in the DB. .tpl.php files are as the name suggests used for templates. E.g. block.tpl.php is the template for all blocks.

If you have 2 distinct type of template for blocks then you could certainly create a block-alternate.tpl.php but there is certainly no need to create specific templates per block.

If you want to alter user input then add fields to your custom content types, or maybe look at the Webform module.