Benefits include being able to see quickly cells who's values are completely wrong or off (giant spikes in graphs). This can be done also with similar success by color-coding the map cells as MegaTune does. If the 3D map is present however, the colors are no longer needed and can now represent something else if you'd like. Or keep the colors. *shrug*
Another benefit of the graph is the ability to see your tune. Really see it come alive. Once you start looking at 3D maps you'll wonder how you ever did without them. It's very easy/common to tune for hours on what you thinks is a smooth, good performing map only to come up with this:

This was what I came up with for DanMartin's turbocharged Nissan SR20 motor without using the 3D map. (Note the spike was an AEM loading error, and was not really in the tune itself).
After getting used to it on other tuning adventures I went back and finished with this:

Again, here's what a well known/respected AEM certified tuner shop gave someone with a turbo SR20 engine:

Areas such as idle and WOT stand out differently from the next, because they were tuned. Everywhere else was a mess. After about 30 minutes of messing around I'd come up with this:

We're all tuners here... Which map would you rather have controlling your car? =D
Now these are pulse width maps (not VE) but the point is made I believe.
On to my next point about being able to grab cells and play with them in a manner of ways.
The second example above took me 30 minutes to re-work in AEM. If I had to do it in MegaTune for VEMS it would have taken me days (yes days) on and off tuning that map trying to get it right, and when I was done it probably wouldn't have been better that the first map I posted. Keep in mind this was done at my desk in my office away from the car using references of idle and WOT known to be decent and filling in the rest. Do that cell-by-cell and tell me how sane you come out on the other end.
Here's examples of what I'm talking about with cell selection and manipulation:









There's a few things I notice now it doesn't do that (maybe) would be nice. You can't hold Ctrl and click on cells to select a random bunch of cells. It only seems to let you select in a "rectangle" so you can select rows, columns, or boxes, but not a speckled pattern (obviously you lose the ability to "calculate ______" with this type of selection).
Take note there's more options I didn't show like "function" which applies a function to each cell with any letter like x referring to the cell's current value. I don't use that one much, but *shrug*.
I'm running late for a movie so I've got to go, but let me say this. If you've only ever tuned with MegaTune or something similar you really need to at least open AEM Pro and manipulate some maps. It's an eye opener.
Oh, and sorry about the image quality (colors are way off). My hosting place doesn't take PNGs.