Let me restate my original point: If 3D can be done without making it impossible for joe gamer to still be successful, I'm good with it.
How do you define successful?
How does giving players the
option of utilizing 3-D space limit joe gamer's ability to be successful?
Take Homeworld for example. You
can play the game quite competently without ever holding down the Shift key (shift was for z-axis movement). This is good enough to play the single-player campaign, good enough to play skirmishes against the CPU, and is good enough for online play against most players on most maps. But the shift key is there for people with the desire and skill to use it. And for those people, it adds a world of freedom and possibilities.
All that is necessary (imo) to give Sins the option of 3-D gameplay is to:
1. allow 3-D placement of orbital structures and
2. give players the ability to choose where their fleet decants from phasespace.
To get an idea of what I mean for #2, consider this (very lame) picture:

The yellow circle represents the boundary of a gravity well. Point A is where your ships currently are. Line AB represents the direct path to the gravity well. This is the current implementation in Sins. It is also what Joe Gamer is going to use (it would be the default). But it could be optional to choose more specifically where your ships go. You could tell them to come out of phase space at point C, or D, or somewhere in between. Rotate this in 3-D and you get a cone of possibilities. (I am assuming that they eliminate the ability to jump through gravity wells so you would not be able to get to a point that is past the tangent line from your current location to an edge of the target gravwell, such as point E).
Now, this would change how some other things work too: first of all, it is now much more difficult to defend your planet with stationary weapons (i.e., the gauss cannon) because you have no idea which direction the enemy is going to come from.
The remedy to this is to 1. change the way you build:
Instead of piling gausses at the star lane exits like you do now, you are going to position them close to the planet so that you can shoot at anything that moves into bombardment range (the inner rim of the gravwell is a lot smaller than the outer edge) and you are going to put them near other important orbitals (which is, imho, a more interesting setup anyways).
Another thing that you could do is increase the range of the gauss cannon (and the other races' analogs). This way you get more coverage from a single unit. In conjunction with or instead of this, you could decrease the cost of each gauss to give you greater coverage for the same amount of money... the details of that would be for the balance team to iron out.
You could also make orbitals take up a larger space, meaning they have to be spaced farther apart than they currently do. This is to prevent someone from building a literal wall of stuff to block the paths of ships. By adding 3-D you now have a LOT of extra space to build in so increasing the space that they take up shouldn't be a problem.
I don't think that these simple things would cause Joe Gamer any problems because he never needs to use them (heck, he might not even realize that they exist) but will make this game much more enjoyable for the more hardcore gamers.
Now, a Joe Gamer who comes up against a hardcore gamer who is utilizing the 3-D space is likely going to get smashed. But then again, he was probably going to lose to the hardcore gamer anyways. And, with Ironclad Online's matchmaking system, Joe gamer isn't going to come up against hardcore gamers anyways. He is going to come up against other Joe Gamers who are equally oblivious to the 3-D possibilities. As he moves up the ranks, he is more likely to encounter someone using the 3-D space. So, if he wants to continue to move up, he will learn how to use it effectively. On the other hand, if he isn't interested in moving up, he won't. Most Joe Gamers aren't that competitive anyways (otherwise they would be hardcore gamers).
Well, that's my 2 cents.