Mini Plus Upgrades  

The only upgrade I recommend is the Bondtech dual drive extruder, which makes the printer much less sensitive to different filament types and brands. The Trianglelab clone is $30, worth every penny.

I know many people swear on upgrading the heatbreak to a stainless steel one (eg Bondtech) to address heat-creep issues, but I haven't experienced any on my Minis with the stock heatbreak, so the Bondtech ones I bought are still sitting in my drawer.

Beyond that, I consider everything else cosmetics. 

The only other suggestion I have for something that makes a meaningful difference—and this is not strictly an upgrade to the machine itself—is to put it on a 16 x 16 concrete paver, with sorbothane feet underneath, to minimize vibrations and noise. 

Agree

I agree with @fuchsr.  I upgraded the extruder to a FYSETC dual gear extruder and it is really nice.  Those are only about $15.  I also don't like the fittings Prusa uses, but that is personal preference more than anything.

Extruder

I have only got the Bondtech extruder upgrade. I have their heatbreak in the spares-box. (was too cheap to not include at the same time due to shipping).

Still on my original fitted ptfe in heatbreak and between hotend/extruder. Put 2 rolls petg, half roll abs, half speel pla thru it so far.

I did put some oil on the first 200mm extruded filament to get the inside of ptfe-tubes, heatbreak and nozzle lubed up.