Wow, lots of questions.  

Basically, combat doesn't work as you describe. Fleets will attack the "weakest" vessel on the opposing side until it's destroyed (weakest being variable based on the types of offense/defense being used, etc.). So formations and creating lines doesn't come into play at all as you described - it's not tactical combat. That said, there's still quite a lot that does factor into fleet combat and ship design.

The enemy AI is pretty advanced, though what it will do is based on the race involved and the difficulty level you're playing at. It doesn't just pump out the same thing, it will adapt.

Allied ships won't factor into the combat in this situation, but there is a United Planets ability that if enacted allows allied starbases to help out in combat.

Hope this helps.

Could I create a front line of heavily armored and shielded ships to absorb the enemies attacks, while I have a rear group of missile armed ships to provide the firepower against the enemy. Will the computer put my ships in this formation?

First of all the ships must be combined into fleets to get the cumlative power effect. You could use the strategy mentioned but it would probably be at lower difficulty. Your comment implies that you will have the tech available to use the strategy. In a high difficulty game the AI will focus on one attack and one defense and they will get powerful very quick. In a long game you might eventually get to that point but early on you will be hustling to outguess the AI and get the techs to counter their power.

Will the enemy AI create diverse fleets of ships?

They will keep throwing the same thing at you as long as it works. If it doesn't work they will make peace and work quickly toward a counter plan.

And suppose my ships and an allies ships are in the same system and or planet orbit. If an enemy ship arrives, will the ally assist in battle?

The battles are always between two opponents. Your ally might fight the first or after but two cannot gang up on one.

I am not a great player and I am just getting around to playing at Challenging. I can beat the AI easily at Normal and below but they are sharply better after that. In a recent Challenging game I was able to hold off and stay close with the Yor due to making some right choices early but they out research me and out economy me. I saved the game after they sued for peace but based on the trend, I will likely lose.