Experience. Also Im not sure they were even, maybe thats stated in the manga but in the anime Vegeta confidently tells Cell that Trunks is almost as strong as he is, as far as Vegeta is concerned Trunks is weaker, albeit not by much. Trunks only believes himself stronger because of the grade 3 form. But he realizes later that even Vegeta must have realized that forms flaws and thats why he didnt bother utilizing it, revealing Trunks naive thinking.  In addition to these points, Vegeta wouldnt hold back in the fight. Trunks would. So with Vegeta being overall stronger, more experienced, and holding nothing back, hed win easily.