Of the officers in Indian Territory, I believe Phillips was the most successful in managing and providing for both soldiers and citizens. Of course, he had the advantage of actually having a reliable supply source, adequate weapons and ammunition, and adequate clothing for troops -- not to take away from what he accomplished under very difficult circumstances. I think he was also an effective military officer, both in administration and in battle. He earned the trust and confidence of the Indian citizens and soldiers.
I think Watie is fascinating -- not as a military commander but as a leader. I think he kept his regiments and the Southern Cherokee civilians intact through the power of his reputation and personality. It is amazing that he held together his regiments and people with hardly any arms, ammunition, food, and clothing and as exiles from their country.
As for the best soldiers in IT... On the Union side I'd agree the well-equiped Kansas cavalry under Blunt and Phillips performed well. The 1st Kansas Colored distinguished themselves at 1st Cabin Creek and at Honey Springs. The 3rd IHG performed well and was reliable and active. On the Confederate side, perhaps Bryan's Battalion was one of the best. I think both the Cherokee regiments performed reasonably well. The 1st Choctaw & Chickasaw distinguished themselves at Newtonia.
Ken