Part of the reason for the clash nowadays is that, when the "invite parents' friends before couple's friends" tradition grew, families weren't as fragmented (geographically, and sometimes with regards to relationships) as they are now. So, traditionally, the bride's parents threw the wedding, and invited their friends as the heads of other families in their social circle, who would welcome the bride to her adult social life. But these were not merely her parents' friends, they were usually the parents of her friends. Even if not, she'd probably met her parents' friends frequently while growing up, so there was a sort of social continuity.
Nowadays, of course, it's quite possible that the couple's friends and their parents' friends are two completely separate circles. This takes away the sort of social bonding that was created by the multigenerational guest list of earlier days.