according to
http://nuggetbridge.com/damagecalc/ Mega Gengar has totally no chance.
252 Atk 252 SpD Jolly Mega Beedrill Drill Run vs. 0 HP / 0 Def Timid Mega Gengar: 124-146 (91.8 - 108.1%) -- 43.8% chance to OHKO..
252 SpA 253 Speed Timid Mega Gengar Shadow Ball vs. 0 HP / 0 SpD Jovial Mega Beedrill: 102-120 (72.8 - 85.7%) -- guaranteed 2HKO
(102, 102, 103, 105, 106, 108, 108, 109, 111, 112, 114, 114, 115, 117, 118, 120)
So Mega Beedrill wins with 40 50% HP left at worse and 70 80% Hp left at best.