UPDATE 12/04/20. This case also works with SKR 1.4.

UPDATE 12/12/19. I uploaded .stl files of Ender 3 and Ender 3 PRO case with 4020 fan. Look for the '4020fan' in the file names. To avoid confusion, you will need to print:

Ender 3 with 4010 fan (stock version of fan):
Ender3_case.stl
leg.stl, 3x
Ender3_cover_left_2.5mm.stl AND Ender3_cover_right_2.5mm.stl
OR
Ender3_cover_left_3mm.stl AND Ender3_cover_right_3mm.stl

Ender 3 with 4020 fan (20mm thick fan):
Ender3_case_4020fan.stl
leg.stl, 3x
Ender3_4020fan_cover_left_2.5mm.stl AND Ender3_4020fan_cover_right_2.5mm.stl
OR
Ender3_4020fan_cover_left_3mm.stl AND Ender3_4020fan_cover_right_3mm.stl

Ender 3 PRO with 4010 fan (stock version of fan):
Ender3PRO_case.stl
leg.stl, 3x
Ender3PRO_cover_left_2.5mm.stl AND Ender3PRO_cover_right_2.5mm.stl
OR
Ender3PRO_cover_left_3mm.stl AND Ender3PRO_cover_right_3mm.stl

Ender 3 PRO with 4020 fan (20mm thick fan):
Ender3PRO_case_4020fan.stl
leg.stl, 3x
Ender3PRO_4020fan_cover_left_2.5mm.stl AND Ender3PRO_4020fan_cover_right_2.5mm.stl
OR
Ender3PRO_4020fan_cover_left_3mm.stl AND Ender3PRO_4020fan_cover_right_3mm.stl

UPDATE 28/07/19. I uploaded .step and Fusion 360 files for all components. Please acknowledge my work, if you are going to remix and publish this model.

For those of you who need an easy and fast access to the motherboard, I included a small rail insert. It will allow to hold the top cover properly in place without screws. You can print one or two of them and put into the central 2020 rail. See photo attached. Note it is asymmetric, so you will need to put it in the correct orientation.

UPDATE, 29/06/19. I added Ender 3 PRO version. I note that in PRO version left side of motherboard is 24mm further away from the fan comparing to non-PRO. To keep far left steppers cool, I reduced the number and moved ventilation openings further to the left. Please keep me updated, if PRO design works fine for you.

This is my take on SKR 1.3 control box for Ender 3. I did not like existing designs and wanted something simple and easily printable without massive supports or board being in awkward position. I use stock 4010 fan, which blows air directly to the drivers. I find it more than enough for cooling my 2208s, although this design could theoretically accommodate 20mm fan version. Uploaded model includes a couple of improvements in cover attachment comparing to what is shown on photos (I am too lazy to reprint the box :)). The display wire could be hidden by attaching it to the aluminum rail with zip ties.

There are two versions of top covers – 2.5mm and 3mm. The latter is also reinforced from inside. If you part is coming out slightly bent, you can print 3mm reinforced version to keep it straight.

Please note, that due to different layout of wire connectors on SKR board comparing to stock Ender 3 board, you will need to extend heated bed power and thermistor wires by 10 cm (at least I needed to do this on my Ender 3). For heated bed you need to use appropriate wires rated up to 10 amps (I used AWG 18) and do good soldering.

You will also need:
4x M3 nuts for cover. You will need to hot mount them.
2x M3 nuts and 2x 15mm M3 screws (longer if you’ll use a fan guard) to attach the fan, although I just used hot glue to mount it.

I printed case with 35% infill and cover with 20% infill. Support is only needed for fan opening. You will need to print 3 legs to insert into the bottom of the case.

I used SKR v1.3 Mockup Model by towe for my desing.
https://www.thingiverse.com/thing:3701548

If you worried about open fan, just find and print some 40mm fan guard. For example, this one.
https://www.thingiverse.com/thing:2335067