catalog_product_flat indexing take too long time.
How to make this indexing faster in Magento 1.9
You can't speed the process. Barring any errors on your site or any 3rd party modules that are affecting the speed of indexing, if you have thousands of items and hundreds of attributes that are getting indexed into the flat table, it's going to take time.
You can look into modules that provide asynchronous indexing like this one from mirasvit