Jake has fought ghosts in his universe but that doesn't mean he's completely prepared against Danny. The only thing the ghosts had were intangibility, and lacked the dozens of other powers Danny had. Plus, the ghosts of Jake's world were magical creatures, while Danny's ghost powers came from a science accident, not to mention most of the ghosts in Danny's world aren't deceased beings like the ones Jake fought, Danny himself is not a magical being. It's too big of an assumption to say that means Jake's immune to Danny's intangibility.
Danny did actually knock out and defeat the dragon in "Parental Bonding" before removing the amulet, he didn't have to remove it immediately to defeat Dragon Sam. He threw her nearly a mile to get enough time to overshadow his dad and beat her to submission to the point where after he wrapped her up in the fishing rod (the only purpose of which is to wrap up ghosts) She was knocked out. that arguably means Danny had more experience fighting someone like Jake and winning than in Jake's case, as you point out Danny stalls a lot in defeating his enemies to trap them in the Fenton Thermos, but that's EXACTLY what Jake did with the ghosts in his episode. He used the plot mcguffin to beat them rather than actual skill, not to mention Danny's physically beaten ghosts without having to trap them in the Fenton Thermos. The Dragon Danny fought has much more simlarities to Jake than the ghosts Jake fought. The only thing the ghosts had were intangibility and a little flight, which Jake was immune to because once again, magic. The dragon Danny defeated had super strength, speed, durability, and fire breathing. Which one sounds more applicable?
Danny not knowing about the weakness of Jake doesn't mean that he can't beat up Jake regularly with his super strength and ghostly powers. Jake's been knocked down by other attacks that don't rely on either of those things. He's not Superman where his durability is big enough to survive exploding cities. Plus Danny could easily exploit Jake's arrogance. Sure Jake knows when to get serious, but he's shown to be way more cocky with his abilities and by the time he gets serious it might be too late. If he's putting Jake at withstanding 400 lbs as strength or durability, Danny's shown to eclipse that a number of times.
"Danny's a ghost meant to fight ghosts." All right, if there was absolutely ZERO variety when it came to Danny's ghosts you might have something, except that Danny's ghosts still have super strength, flight, speed, and a variety of weapons and powers. Only thing that really makes them different from typical superhumans is their intangibility and ectoplasm, which some of the ghosts don't even utilize. It doesn't make Danny's strength and durability moot against anyone else.
Danny never defeating Vlad might be the biggest nerf on here. Vlad's had much more years to perfect his ghost powers and considering how close Danny's come to defeat him physically a number of times, that's pretty damn impressive, especially when he beat his future self (that was a combo of Danny and Vlad who's ghostly wail could take down a city wide ghost shield) He also matched Vlad in combat a few times in infinite realms. Would Jake defeat Vlad in their first encounter? Probably not. Let's not forget that Jake's had to rely on his allies a number of times for his victories for foes such as the Dark Dragon. Focusing on Danny's constant losses to Vlad is still a lowball, especially the "he lost in an alternate timeline," excuse. Because Jake's NEVER struggled against people who have peak human abilities and know techniques and have weaponry designed to take him down before... oh wait, he has.
A number of Danny's ghost powers were not considered for the final result or the fight, such as overshadowing, spectral body manipulation, his healing factor, power augmentation, telekenesis, ghost shields, etc. Plus they have great destructive power. Danny was able to freeze the entire city in seconds.
It could be argued that Danny held back his ectoplasmic powers on the humans as well as Jazz with her blast, as they don't have kill codes. Plus Jazz only knocked out Vlad in deceit when he wasn't in his ghost powers, she can't defeat regular Vlad. Considering that a number of Danny's ecto charged attacks can emit flames and can break through metal, let's just say that not all the attacks are only damaging to ghosts.
Jake's training over Danny isn't that much of an advantage. They both got their powers around the same time and Jake's only trained for a couple years, while Danny's self taught enough to deal with skilled combatants in multiple weaponry, not to mention Danny's slightly older. If we're going by general knowledge, Danny takes it from his scientific experiences and the fact that he's older and had more education. Fighting style is debatable as they've both shown great combat in their super powered forms, Danny's even shown to be a good swordsman. But he chose the low end for Danny once again. Jake having the better strategic mind also lacked explanation and makes no sense, especially since he said that Danny's mind was one of his most powerful weapons in this fight (aside from all the powers he chose not to use that I listed above). Danny's shown to be a proficient leader and comes up with detailed plans on the spot, I'd say Danny either takes this given his experience and age or it's a tie.
Danny's had better speed showings than 112 mph than the plane feat. Plus Danny only went a short distance and he hadn't fully mastered his ghost powers yet. He flew from 12,000 feet in the air back to earth in a few seconds... in the first episode. If we consider how high planes fly, he was knocked into the air about as high as an airplane flies in just a few seconds, which I can imagine requires a little more than just a few tons of pressure. Then there's the space station feat that he counted as PIS.
Really the only advantages I see Jake having are better trainers and not losing his dragon form when unconscious. Danny takes it in strength, durability, destructive capability, and offensive and defensive options. I don't think it's quite fair to give Jake the speed advantage when you consider my explanation above.