Anime Pure Boo > Super Vegetto

[Pakl]

Episode 281
Context: After Boo catches Goku's leg with his stretching arm from underground and tosses him inside
Goku: "You truly are strong! Even greater than I imagined."
Boo: "Gonna kill you!"
Goku: If I had known it was going to turn out like this.... I should have finished you off for good when I had become Vegetto. But no matter what, I can't afford to lose!
Note: Goku seems to imply that Pure Boo is stronger than Super Vegetto as he said "I should have defeated you when I was Vegetto" and not that he should have used the Potara to win. This is further implied when in the anime, when Goku tells Vegeta that he got all arrogant and he thought it would work better, but doesn't mention the manga line that if it was with the Potara, he would be able to beat him with one shot.

Episode 281
Context: Vegeta tells Goku he can obliterate Boo at SSJ3 if he gathers enough ki
Vegeta: "Don't hold back for me, finish him off! With your Super Saiyan 3 there, if you gather as much ki as you can, you should be able to completely obliterate Boo!"
Goku: "Yeah... I've been thinking of doing so for a while now, but I just ain't had the chance. [ ] Here I'm wanting to obliterate him, but I have to gather ki for about a whole minute."
Vegeta: "One minute?"
Goku: "Maybe I've been trying too much to look cool! thought things would go better than this!"
Vegeta: "Y-You were concerned over me?"
Note: As I said, the line of being able to beat Pure Boo with one blast with the Potara was removed.

 

[Spiral-Force]

Note: Goku seems to imply that Pure Boo is stronger than Super Vegetto as he said "I should have defeated you when I was Vegetto" and not that he should have used the Potara to win.

Finishing someone off doesn't constitute winning?

This is further implied when in the anime, when Goku tells Vegeta that he got all arrogant and he thought it would work better, but doesn't mention the manga line that if it was with the Potara, he would be able to beat him with one shot.

One of your own quotes goes against that. Look below:

Vegeta: "Don't hold back for me, finish him off! With your Super Saiyan 3 there, if you gather as much ki as you can, you should be able to completely obliterate Boo!"
Goku: "Yeah... I've been thinking of doing so for a while now, but I just ain't had the chance. [ ] Here I'm wanting to obliterate him, but I have to gather ki for about a whole minute."
Vegeta: "One minute?"
Goku: "Maybe I've been trying too much to look cool! thought things would go better than this!"
Vegeta: "Y-You were concerned over me?"

Conclusion: Super Saiyan 3 Goku has the power to put Kid Buu away, but he wasn't fighting efficiently. The whole point of Vegito was to utilize power that exceeds his fusees, giving them an opportunity to clean up their mess when the bad guy is too dominant. On top of that, he doesn't have to deal with the strain associated with form 3 like Goku suffered.

 

[Warmmedown]

It's just saying Kid Buu is too strong for SSJ3 Goku to easily beat so he should have beaten him when he was Vegito. It doesn't make Buu stronger than Vegito. Just anywhere between around SSJ3 Goku and at most as strong as Vegito.