If Primal Groudon is not running Dragon Claw then, Mega Rayquaza, Giratina-o, Giratina-a can do well against it.
If Primal Groudon is running Dragon Claw then it probably is forgoing Stone Edge / Rock Slide, in which case, Ho-oh walls it.
A lot of Uber Pokemon are like this, where there are no true counter or none until you have figure out what set it is running. This is nothing new, so while I do think Primal Groudon is a very good Pokemon, I disagree that it is this overly powerful threat that severely limit teambuilding or is a Pokemon that is way too difficult to deal with.
Other Pokemon that check Primal Groudon in general are Lugia, Groundceus and physically defensive Yveltal which can check Primal Groudon decently most of the time. There are also some obscure checks such as Mega Gyarados.
On the topic of Primal Groudon I think Adamant should be preferred over Jolly. Or if you want more power from your Overheat, a Lonely nature can be good too.