Will the speakers be sitting on your desk or will they be on stands off the desk? If they will be on the desk, like mine are, you need to consider the footprint of the cabinets and how much room they will take up. One way is to make a pair of cardboard mock-ups for each of the cabinets you are considering then put each pair on your desk where the speakers will be. This will let you see exactly how each fits on the desk and into your workflow. I find the mock-ups much more helpful than trying to visualize the actual impact of three dimensional measurements. On my desk, the speakers flank the monitor. I've had X-LS Encores on my desk and found they took up way too much real estate to suit me. The LGKs fit perfectly.
Another consideration also related to where the speakers will be placed, is the distance where the sound comes together. In a desktop setup the speakers are usually not much more than an arm's length away. I found this to be too close for the X-LS Encores to gel properly. They sound much better at least 5 ft from my ears. The smaller single driver LGK did not have this issue and sounded excellent at arm's reach.
For bass performance, the Encores play lower. However, I found that on the desktop the bass performance of the LGKs was astonishingly good. I've had them set up at the Lone Star Audio Fest a few times and everybody that listened to them did a jaw drop when the bass came in. A subwoofer is not actually necessary and I ran mine for a few years without one. However, adding a small subwoofer under the desk fills out the low end very nicely. My LGKs are the 1.0 model. I haven't heard the 2.0 version but Hobbs says the bass performance of the 2.0 is better than the 1.0.
Taking everything into consideration, from my perspective, if the speakers are going to be on the desk close to you, the LGK would be my recommendation. If they are going to be off the desk on stands and farther away, the X-LS Encore would be the way to go.
The LGK 2.1 adds a midwoofer which gives more bass extension but increases cabinet size and brings in the distance issue for the two drivers integrating. For a desktop application, I'd stick with the smaller single driver 2.0 and add a small subwoofer if you want more bass extension.
With the X-LS Encore the "version" options are Bookshelf (X-LS) and floor standing (X-SLS). The larger cabinet provides deeper bass extension. Otherwise, they are the same speaker.
Here are the LGK 1.0s in a desktop setup
The black speaker is an X-SLS Encore
