Just a idea but if A3 are looking to merge or work closer with another airline couldn't they link up with TK in neighbouring Turkey.
At present TK is part of * Alliance which Aegean will join in May.
TK currently operate a ever expanding worldwide network. Where A3 mostly operates to European destinations west of Greece. Both currently compete on the IST to ATH route. With TK operating 3 daily flight and Aegean a daily service.
Say TK bought a fairly large stake in A3. This could allow TK in the beginning to use A3 as a feeder airline for it's expanding longhaul network ex IST. TK could come to a agreement with A3 whereby A3 took over the operation of all the IST/ATH flights and TK would codeshare on them. Also TK could codeshare on A3's domestic flights to and from ATH.
In return the A3 code could be added to TK's services to the Middle East, North America and Asia as well as those European cities where A3 currently don't operate to. With tickets available for sale through both airlines.
By doing things this way both airlines could keep there seperate identity while at the same time generate more revenues and increasing market share.