Hi Guys, I personally as an ATC prefer the regos. But there are probably ATCs that prefer flight numbers, so dont take my opinion (this time anyway) as gospil :-)
Think there can be a number overload using FNCs, and possibility of 2 companies having same number (eg QANTAS113 and Virgin113) and chance of pilot or ATC not hearing properly and assuming wrong aircraft when busy.
Tho, one advantage of flight numbers will be calling up details on the TAAATS system. If an actraft is using a rego, and someone calls up and asks for an ETA on a flight number, we cant do a search for it. Can only search on callsign aircraft is actually using.