Some good comment here. While some of you definitely have a finger on the pulse of the problem, none of you have identified the real reason.
Is Sweden money-wise (and all that goes with that) better then Denmark? –Yes it is. Is that the reason Sweden overpower Denmark (and everybody else around him) in most games? –No
In MP games this is probably the reason, but not in single player!
The trick to this is simply so easy that it hurts, it is btw the easiest fix, of all, in the greatest ai mod.
Sweden is a raging warmonger, with a staggering 60 in war setting, surpassed only by Spain, Russia, Turkey and France, having DAN, NOR, RUS, LAT and POM on the ‘job’ list.
He can’t fall on Denmark for about 100 years (normally); he can’t fall on Norway, cause Denmark keeps him in the alliance, only occasionally can he sneak in on him, when Norway dishonours, which he does often, as he is not a warmonger. But Denmark normally keeps him safe, by keeping him in the alliance. He does not have a border with neither RUS, LAT nor POM.
So what does a ranging warmonger do, with no option of attacking his job list ?? He falls on the 2nd best, which is ~ drum role ~ yes you guessed it NVG. The only nation Sweden can attack via land.
All the Russians states are warmongers too, 100% in fact, have all of each other on the job list (all using the Russian ai file) so a war will fall up there within 1 month of the start of the game, with a 100% involvement of NVG each and ever time.
You got the only target of SWE, currently in a war – of course SWE declares war on NVG. It happens again and again.
This led 99% Denmark into the same war too (Norway maybe 50%).
By the time someone has gotten the upper hand up there, its time for SWE to set it self free from Denmark, automatically leaving Denmark as supreme and only target available for SWE.
SWE has the money (province, tech, ducats, leaders), the will (warmonger), the opportunity (DAN provinces is available all around him) and the reason (job list).
Like Amen in the church. Denmark does not stand a chance.
It is not the money the leaders, the tech and provinces riches – that is only the things that makes him able to do it in the long run. Denmark ALWAYS loses exactly because of long wars.
It is the will and reason that do it. E.g warmonger and job list.
Set the Swedish war to 10 and remove all from the job list for 130-150 years – and you got a historical SWE playing right before your eyes

Up his war later, but you should not put DAN on the job list before 1600-1650.
With these simple changes you have corrected both DAN and SWE in one go to dang near historical play.