For me, one of the biggest issues was support. Am I going to actually get one when I pay for it? Lots of folks had paid Gearbest or whomever for their CR-10, only to be stuck in limbo, and then have to try and get their money back.
Heated bed on the Prusa. Not that the CR-10 doesn't have one, it is just that the Prusa's heated bed is just that, the bed and the PEI coating (tape, albiet one homogeneous layer). No glass plate in the middle to mess with. I had worked with a SUPER early Lulzbot (Ao-101) which was an expensive machine in its day. The heated bed on the Lulzbot sucked in my opinion, and I when examined pictures of the CR-10, it appeared to have the same bed system.
Z system. With a build area that big, not sure how they get the accuracy that they claim with only one side driven.
The hot end on the Prusa is pretty much ready set go. It will print almost anything you can throw at it, although I have only printed PLA and PETG. Both stuck to the PEI beautifully with no "juice" treatment. The Prusa has bed (actually head) adjustability that will just make you smile. I printed a 4 square pattern on my Prusa, carefully examined the print, and could level the bed by a 20 or 30 microns to really dial it in. Maybe you can do that on the CR-10 but I doubt it.
As I mentioned before, support was a big issue for me, and part of the support that is "baked in" to the Prusa is the Prusa Control software and Slicr Prusa edition. Both have the Prusa printer integrated into the slicing program and I will have to say it works pretty much flawlessly. In fact, when I first started using PrusaControl, I felt there wan't enought options/settings to give me control, but I quickly found out that I really did not need to mess with the settings hardly at all because the Prusa team already had them dialed in to the program. And yet, if you want to, you can fire up Slicr Prusa edition and it will give you a lot of control over your printing.
The two things that I do like about the CR-10 is print size and the linear roller bearing system that they have for their axis movement. Prusa uses LM8UU linear bearings, and I personally do not think that they are very good quality at all. Sure, they work, but it is louder than it should nor needs to be. One final nudge for me towards the Prusa was the fact that my daughter's future brother-in-law has four 3D printers. Two of them are Makerbot Replicator+'s and the other is a Prusa. He told me he wished he would have just bought the Prusa due to ease of use, and cost vs performance ratio.
I am sure that the CR-10 works great for a lot of people. I am just really happy that I went with the Genuine Prusa i3. I will be doing the upgrade to the 2.5 here shortly.
Prusa vs. CR-10
Here is a reader's comment from the video below. Not mine but ...LOL
"cr-10 takes all from the reprap community and gives nothing back. They are a parasite. Prusa ontinues to add to the reprap community"
Prusa i3 Mk2 and the CR-10