for me I never had overheating problems, but I had water pump leakage, so I replaced the pump, belt tensioners, and thermostat with aftermarket thermostat.
I even indexed the thermostate so the weep hole was where OEM was.
a couple days later I was towing a 5x8 trailer that weighed in around 1000 lbs loaded. the jeep overheated within around 18 miles and top of radiator split out.
yes the thermostat was installed facing the correct direction
this time I put new radiator (Mishimoto since OEM can't be found). new hoses and this time I put in an OEM thermostat and a new thermostat cover for the **** of it.
no problems since. I towed a 2500 lb boat this weekend and left it in OD and watched the temps, no rise at all.
so yes I also believe some aftermarket thermostats can cause problems.