The players do seem to speak highly of him. Spurr was almost gushing about Lyon in his retirement video, and he thought the future was bright.
I always think these things should be taken with a grain of salt. Even though he was retiring, there's no benefit to Spurr throwing his old coach under the bus. Still, if he didn't rate Lyon, he was laying it on pretty thick.
I can't remember reading many stories about coaches getting on with their assistants, so I would be hesitant to speak one way or the other. Kirk returning to Sydney is viewed now as evidence of Lyon being difficult to work with, but that wasn't raised at the time - the way no-one has really questioned Mitchell leaving West Coast two years into what was supposed to be a longer-term arrangement.
I think Sumich was at Freo for 5 years. That is a long spell by assistant coaching standards, especially when that assistant had (unrequited) designs on being a head coach. I would have thought that new blood could only have been a good thing after the start of 2016.