What is the difference between enhanced and not enhanced troops?

Enhancing the troops, which is done in the Command Center Building once you have unlocked if via research in each troops type), will improve the stats on the troops a little. You can see the changes that will be applied to the stats when you tap the enhance option.

In general the attack and defence stat will increase, but not as much as reaching the next level of troops. So Tier 5 < T5 enhanced < T6 < T6 enhanced etc.

Enhanced troops also heal faster and cost money to heal.