I admit that the function allowing people to automatically equip the mods is not a bad one but I am not sure if the recommendations they have listed are the right ones or even take in to account the all the secondaries on mods when it recommends a mod for placement.
For instance my arena team with Darth Nihilius has a 14+ speed gold mod with solid other secondaries yet it says in should replace it with a grey mod and no speed also less worthy stats. This suggests that the system is just placing mods off the primary attribute and none of the lesser ones which some would argue are more important.
Secondly I don't know if the recommendations made by the mod advisors are even correct ones for the Toons. I have a feeling that while some maybe generally right the rest are off by miles. I don't think CG bothered to do any research on mods and Toons. They could have simply got with some of the leading mod sites and worked with them to develop the mod advisor.
The recent changes remind me Heroes of Dragon Age and how they game went downhill so quick. Players even banded together to provide the underhandness going on with solid proof. Always that is another conversation.