Considering that Humanity in FS2 has been waring war in space for centuries they won't be surprised by an enemy who uses all three dimensions. If there is any reason to twodimensional mission design, then it's due to the mission creator, not because of any background story.
Well, seeing as we've barely seen radical use of the Y axis in
most campaigns, retail included, I'd daresay it would still effective. The point was, to use something the enemy has never seen before.
Unless it is a very broad and flat formation it really doesn't matter if an enemy is coming from above or from the sides.
Disagree. Look at FS2 ships, their firepower is focused predominantly forward, broadside, and aft (in some cases). If you can hit the enemy hard before he has time to maneuver his gunners into a position where they have a firing solution, you've got the upper hand. And the intention in my poorly thought-out strategy before was to split the formation up.
Actually I would think it would be smarter to hit the enemy not form two directly opposit directions, but rather have one group attack from left or right and the other from above or below to minimize the chance of the two groups hitting each other with the shots that miss the enemy formation between them.
It also leaves you the tactical option of uniting the two groups if the situation calls for it. If you have the enemy directly between your groups that's not an option.
Uniting the two groups in a three dimensional environment is a no-no in my opinion, because you now become very easy to outflank. But if left and above is a formation that works for you, go for it.
Jumping in Deimos in the middle of the enemy formation also doesn't sound all that smart to me, considering that the mainline battleship of the UEF, the Karuna, has quite powerfull broadsides. Jumping them in behind the enemy formation would make more sense to me. Same goes for Shivans. If you jump the corvettes into the middle of the enemy formation they are bound to be in front of some ships. And a Deimos in front of a Shivan ship has a rather short lifeexpectancy.
Of course it's a stupid idea! It was the product of two and a half seconds of thought!

By the way, the Karuna is a frigate, and believe me, far from the most common ship in the Federation.
The idea was, the initial assault has resulted in your enemy commander splitting the force up, to deal with the separate threats, since well, staying as one large group is generally a stupid thing to do, when facing a Titan and a Raynor (and taking into account their firepower and where it is).
This results in your enemy formation now being two formations. Once the gap is large enough (your destroyers are taking it slow, to give the UEF time to move apart to create the gap without opening fire), you jump your corvette pair in here, who then peel off and engage a UEF formation from the rear each.
Here, your destroyers put the foot to the floor, and within about 10-40 seconds, your UEF force is now confused and in disarray. They can't go back, because there's two TSlashes giving them what for. They can't go ahead, or you'll deal with some nasty looking beams.