I don't have firsthand experience with the Ender 3, but I do with a nice Wanhao i3. I would basically echo Aurich's point. The Prusa MK3 is a printer with a multitude of features out of the box that the lower cost printers just don't have. As a result of the Prusa technology, it delivers the best results possible with minimal effort, including is dialed in Slic3r which I have barely had to adjust compared to the never ending burden that was Cura with the Wanhao i3.
While every analogy has its flaws, you can kind of think of it back in the olden days when choosing between a PC and a Mac (obviously the differences are more blurred today). Do you want a device that requires some expertise, lots of tinkering, complicated methods to achieve certain tasks, etc., or do you want a machine that has been developed to take care of all those things automatically and to make your experience as simple as possible to achieve your desired results?
Can other lower cost printers deliver similar or even better print results than the Prusa? Sure they can, but the amount of time you spend to achieve these results can often be quite expansive, require lots of trial and error, and result in wasted filament, etc. If you are a tinkerer at heart, have a modest budget, and want to really learn the nuances and intricacies of 3D printing then I might encourage you to save some money and purchase a lower cost printer. If you want nice prints with minimal effort and a shorter learning curve then the Prusa is my recommendation. Or, if you are like me, and have experience with learning the ins and outs of 3D printing on a lower cost unit and want to step up to something a little nicer and overall simpler to operate with additional important features (e.g. auto bed leveling, power outage recovery, auto filament detection, ability to print multi-colored layers, ability to pause/resume print, larger print area than many lower cost printers, etc.) then upgrading up to the Prusa MK3 may be a good move for you.