But at the top levels... there's still the same issue as always of using your mega slot on a passive wall instead of a high utility or high power one.
I don't think this is inherently an issue honestly, I think the problem is more that there are no defensive Megas except for Sableye and Audino. Mega Sableye saw some pretty significant success (although I guess you could argue it falls into the category of "high utility" with Magic Bounce, Wisp, Knock, etc.), and Mega Audino's shortcomings go beyond just it taking up your Mega slot.
I think if there were more actually viable defensive Megas, there's not really any inherent reason why they wouldn't see some usage on stall and other more defensive team archetypes, but for whatever reason GameFreak decided to give almost every Mega a heavily offensive bias. Even some that, on paper, might seem defensive, such as Slowbro, are usually used offensively, with Mega Slowbro seeming almost designed to be the ideal Calm Mind sweeper.