Funny you should ask; I had the same type question a few months ago, but didn't get much advice, unfortunately.
My first and only CNC machine is a Microkinetics Benchtop mill, 3 axis, purchased as a "turnkey" system which included a computer, the software loaded, a controller, and power supply. All installed and tuned up by the vendor. I did it this way to simplify the experience as much as possible, and have to go to only one source for answers.
Understand, this is my first and only CNC machine, and may or may not be typical. With a few classes in programming under my belt, a pretty long history of working with CAD programs such as autocad, and about 30 years of machine shop experience, I thought I'd be in good shape.
Generally, the machine has been a real thrill to use, for all the reasons a first-timer would anticipate. However, the unit had to go back to the vendor about a week after I'd recieved it, with a badly aligned X axis motor and a screw coupling that simply wouldn't stay secured. When it was returned it had a few extra superficial blemishes, but seemed to work OK. The X axis anti-backlash nut sometimes detaches itself from it's mounting location, but I've learned to watch out for that and check it frequently. The software is servicable, though I think the grid area where you view the toolpath is a bit quirky. I bought the extended version, which means that the motor/spindle is extended a few inches, giving the machine a deeper throat; more working area. Maybe the motor drive of the Z axis works well with the standard model, but I feel that the extended versions extra reach also distributes the weight in such a way as to put more strain on the motor; consequently I've learned to program upward Z moves at conservative (12 I.P.M.) speeds. At higher speeds the motor sometimes seems to stall a bit and lose its location relative to the home position. The Y axis screw is exposed to any and all junk that spills off the machine; no covers were available, so I made my own.
Right now I'm waiting for a reply from Microkinetics technical support; yesterday the machine started to lose the ability to follow a given tool path repeatedly. None of the previous mechanical problems I've had are evident, it may be something I can't fix, and have to go back to the vendor again. I sure hope not.
So, as sour a note as this is, bear in mind that I don't have much background to compare it with. I haven't abused the unit, quite the contrary. I've had the machine about 4 months, and there's a bit of love/hate going on already.
Tom