I would argue that Thomas’ mistreatment was by Sherman, not Grant. Grant’s only source for how Thomas was performing at the head of the AotC was Sherman’s telegraphs, and Sherman had a habit of throwing subordinates under the bus.Although I agree that Grant's treatment of several of his subordinates including Rosecrans, Warren, Hooker, and most notably Thomas - but also including McClernand, Prentiss, Custer, and likely Hurlbut as well - was often mean and shabby, I seriously doubt that any of them with the likely exception of Thomas didn't to at least an extent deserve it or bring it upon themselves. And as far as any of them - again excepting Thomas - challenging Grant's subsequent reputation, I seriously doubt that too. Grant seems to me to have unreasonably held a grudge against anyone he perceived - correctly or otherwise - to have ever challenged him or stood in his way, especially when it involved tale-bearing or skullduggery of some kind as with McClernand, Hooker, and possibly Rosecrans.
If you can’t tell, I really don’t like Sherman.
That being said, Thomas’ frequency of communication with Grant didn’t help.