Sorry for the large wall of text, you can read my conclusion at the end, but if you wish to see why I concluded that you need to read this nice wall of text. 
The biggest problem of 3D maps it’s the memory usage. Yeah, right? With 2 Tb in disc and 16gb in ram, how my pc can't hold a 3D map? Well, your computer is not the only one that uses memory, you also use memory. It is easier to remember where is Webber II in a 2D space rather than in a 3D one, even from an "overall perspective" (it is on the up-right corner [2D], rather than it is in the up-right-down corner [3D]). 2D and 3D has the same problem of memory usage but, 3D scale too quickly.
(For sake of a nice argument, reducing into a 1D for the sake of saving memory is logical but not fun, right?)
Other problem with 3D maps is the orientation, in order to have a good 3D game (of this kind) you must have a "rotate" function; if you don’t add one, you are completely lost since some solar systems could become inaccessible because of visual obstruction (3D nature), now add the complexity of a 3D map with rotation and memory usage and you end with a headache (kind of). In order for a 3D map to work you must implement some kind of safe guards like a button that fix your view in order to have a better (standard) orientation. Since in a 2D map is hard for an object to block another object you don’t need rotation or a fix button (you might have it, but is not a must if well programed).
Navigation is not a big issue in a 3D map once you have figurate your position and your destination. Now strategically speaking, defend a 3D section is a headache: you need more ships (just to defend a space), you need to cover the front, back, left, right, up, and down of a planet or system (instead of just the first 4) or, do what everyone does, just defend the planet per se (put a ship per planet). That was easy, but wait, what if I have to intercept some enemy ship before they arrive and destroy my defences? Well, I have to do the same as I do in a 2D map, just with more distance due to the 3D nature (and more ship to cover that extra space). Want a quick fix? Warp lanes, space lanes or some restriction that allow you to protect something with fewer ships.
Tactical advantages: you can assault someone from above or bellow, increasing your tactical options. The only downside of this: if the game dictates that the damage is calculates as equally, no matter where the bullet comes from, that tactical advantage is greatly reduced. If you not calculate the damage that way, well, why should I bother with a normal ship with a lot of flaws? Instead, I’ll design a spherical ship with a more balanced defence and attack than a “normal” one (and there is not wind that interferes with my movement and speed due to friction) and reduce that “tactical advantage”.
And let not touch the beauty of seeing your control sphere in a 2D and the problems that that would be in a 3D, especially in a “bird view”.
3D advantages? First, a 3D map is amazing and beautiful in more than one way. 2D can’t be that beautiful (even more than a 2D with 3D incorporated as in galciv2). The complexity of the galaxies you can make in a 3D is awesome. In a holographic room a 3D map would be, well, just orgasmic. If very, very, very well implemented the tactical options would be greater than in a 2D, but you can increase the tactical options in 2D maps as well in many ways.
In conclusion, 2D maps are a simplify version of a 3D map. That simplification reduce the cost in ourselves and increase our effectiveness overall, making the game faster (that is slow as it is), our decision better and focuses our attention into “more important maters”. There are some good 3D games, but there are more 2D games out there (per capita)