The scene really isn't open to interpretation, it's really cut and dry what happens to Cell, regardless of how you'd place them strength wise. Nothing implies Cell is weaker, other than "OH HE BEAT HIM" or "IT'S FILLER". Neither excuses are valid because of the following:
I. Goku beat Pure Buu in SSJ, does that mean SSJ Goku > Pure Buu? No, not even a little. You have to look at how he beat him.
II. So what if it's filler? We can still apply logic to scenes seeing that not every inch of filler is a plot hole.
Taking the whole plot hole aside if Paikuhan were to be stronger, which he isn't, then look at the actual evidence in the fight. Do you even see Paikuhan and Cell fight? No, you see him being taken by surprise. There's nothing subjective or open to interpretation about how Cell's beaten as I stated. This is the same as Majin Vegeta cold-clocking SSJ2 Goku to go and fight Buu. Does this make Vegeta stronger? No, they're very much equal in terms of power in their SSJ2 forms.
If you believe Paikuhan is stronger than Cell, then you create the plot hole of Goku being stronger than Gohan in a matter of days. Not only that, then you're creating supposed animation errors of Cell's power up and sparks being forgotten and even more plot holes revolving around that (There's enough plot holes in the episode that're actually plot holes). It's much simpler to take the scene as it is instead of making up baseless theories, which is, "Cell was caught off guard and beaten". Freeza wasn't taken by surprise really, and even if you wanna say he was, there's no indication he'd be anywhere near Paikuhan's level.
There's no plot hole about Goku being at SSJ2 strength, because Paikuhan wasn't stronger than Cell, simple. Goku charges Cell in his... In between state...? Regardless of how we treat his form, there's no indication he'd even powered up to his maximum from the Cell Games. If he had, Paikuhan wouldn't have been surprised in their fight. Plus, look at Cell. He was likely at the same level as Goku so he could have a little fun, instead of a one-hit overkill. Note there's no sparks around Cell, or even a power up. Note that Paikuhan flies out of nowhere from behind Goku, running directly into Cell; take into consideration Cell's surprised face as he sees it a second before he gets kicked.
It's a very similar moment to Goku and Piccolo Daimao's fight. Daimao wasn't expecting Goku to come at him, Cell wasn't expecting anyone but Goku to come at him. Not to mention that Cell wasn't even charging at Paikuhan, it's not like Cell was being cocky and somehow knew Paikuhan was going to intercept him and changed his course of trajectory towards him. Just look at the episode, it speaks for itself, there's nothing to interpret other than Cell was taken by surprise.
Cell states Goku's strength is nothing, also indicating the reason as to why there's no power up from him.
Cell charges at Goku (No power up from either side, just SSJ Goku, well "in between SSJ" since the animators changed their minds".
Goku is genuinely surprised by Paikuhan interfering.
Cell is discombobulated by what the hell is coming towards him.
Look at the animation very closely. Paikuhan appears from nowhere seemingly, blazing past Goku. Cell catches a glance of this and his eyes widen, within a second later, Cell runs into him full force and becomes unconscious/immobilized from the hits, having no time to react in the mean time. All this said is, Paikuhan's speed allowed him to take out a suppressed Perfect Cell. It's later revealed that Paikuhan is around SSJ Goku's Cell Games post-powered up state. Meaning that Cell would only have been able to beat him if he was powered up to his full power before he got his zenkai; which he wasn't. We don't even have to factor in Super Perfect Cell, because that would be overkill and both Goku and Paikuhan would be defeated easily. Note the fact there's no indication of Cell powering up, being powered up, powering up prior off screen, no sparks or any actual reason to be anywhere more than Goku's level.
Also please take into consideration that Goku never once comments on his strength during the events, only his speed. So let's reconstruct the data above!
Paikuhan who can take a Perfect Cell that'd be suppressed around SSJ Goku's level charges up his attack off screen. Cell in the mean time has no sparks, no aura and no reason to be powered up and takes off after a Goku that isn't even SSJ (His hair was colored black at the last second remember). Instantaneously a flaming silhouette passes by Goku at an immense speed (Goku himself is baffled by Paikuhan interfering and later attributes it to being about his speed), Cell sees the blazing figure a little way from Goku and yells in confusion. He's struck before he has any time react or even slow down, immobilizing him.
The argument of it not being said Cell wasn't at full power and that it's not out right said Cell was taken by surprise is entirely baseless. It's never stated the reason Cell being taken out wasn't because of him being caught off guard either, the only commentary on it is his speed; evidently that allowed him to clock Cell out in the first place. It's also never said that Cell was powered up either, nor is there given at all, any indication. To say Toei cared enough to put an aura around Goku, who mind you didn't power up either, but not Cell because they didn't care, is entirely speculation and strays away from any contextual evidence.
An example of straying of from any evidence would be again, saying that Paikuhan is stronger because he beat Cell. Nothing suggests he's stronger than full power Cell or post-zenkai Cell, in fact it's viably suggested that Cell is stronger because of the various reasons already stated in this post.
I'd like to reiterate the fact that because it's filler, is absolutely no reason to say it's automatically a plot hole. Yes, there's a lot in that episode, granted there's also a lot of story elements that aren't. Saying "It's filler you can't make sense of it" or "It's filler just look at all these other examples of plot holes" has no foundation.
