TokuDB uses a write-optimized data structure. A B+tree like InnoDB is more read optimized (although writes scale well while the key pars of the tree are in memory).
I know you are the product manager and gave a line to tow and all, but tokudb really belongs distributed with stock MySQL. It's a basic enabler for a modern revolution in MPP which perhaps Oracle doesn't want to realize.. ;)
When tables are small and fit into memory tokudb and innodb are damn close performance-wise. But innodb has crap compression so stops fitting into memory a lot sooner, and innodb performance drops off a cliff when it stops fitting into memory. Whereas tokudb just sails on awesomely. It's easy to have multi-TB tokudb tables. Just a shame that the next jump upwards is forgotten-ware like ShardQuery. MariaDB is doing Spider and Tokudb ...
There will always be use-cases for each.