What is the purpose of the team? If it's farming, merlin wouldn't replace Koyan under any circumstance I can think of. If it's a challenge quest merlin would be more valuable. Let me know what you're trying to accomplish and I along with everyone else here could give better advice.

You'll have different answers depending on farming versus challenge comps. That looks fine for a farming comp, though Altria and Koyan's skills should be 10/10/10 ASAP. I'm not sure why most CE slots are empty (I can think of a couple possible reasons), but I want to stress the importance of buying Chaldea Lunchtime if you don't have it already. If you have more rare prisms, buy the Heroic Portrait, too.

Now then. Heracles' strength is in his face cards, particularly after all his strengthenings are done and you have his bond CE. I'd put him in back. Depending on the content, Mash's position could be closer to the from to she can taunt herself and get sacked. Give her and Enkidu Fous when you can.

These are generalities since I'm not sure what sort of comp you have in mind.