He's had better circumstances in most of the cases he surpassed Vegeta. Gravity training was something he pushed to new levels that weren't possible naturally, the focus of refining SSJ rather than achieving new forms seemed to yield greater results in general and training in a new situation will always offer greater GAINZ, which is what he did with the afterlife training as opposed to Vegeta just doing more of the same gravity chamber training for 7 years.
The only case in the original manga which is impossible to argue for is his Zenkai on Namek compared to Vegeta's. Without resorting to "because plot", the most you could do is make the outlandish assumption that the older healing chambers had a different type of liquid that reacted well with Saiyan biology or that bathing in it for a longer amount of time helped release more latent power.
