2nd time this is mentioned and I honestly don't know where you're looking at. On Aegean's own website (which is certainly not guaranteed to offer the best prices for the EK flights!) the A3 flights in P comfort flex cost 557€ return and EK's "comfort flex" costs 685€. (tried some dates in March, like 13th-20th)
For these +64€ per direction I'd take EK's plane without a second thought, even though I'm accumulating miles with Aegean!
Skyscanner shows a difference of around 150€ return, however this includes a 25kg bag with Emirates, while on the other hand it's only Aegean's light fare, so the real difference is mich smaller!
Also be aware, that if you're planning to use vouchers to get upgraded, you'd need at least a flex or comfort flex ticket, since the prices discussed here are for booking class P (not eligible als light, which is also the case for U and T, which are currently mostly available for sale).
Business class is around 400€ or 30% more expensive on Emirates.