At release and for awhile afterward. According to Eric, during the initial development of the game, it was Classic APs. Then through conversations with Uwe and with his blessing, it was removed and Persistent APs was created to give a different style of play than the board game.
As a lifelong comic book fan, I can tell you from personal experience that anything that fractures a fan-base can cause more harm than good, depending on how it's handled.
With the release of the PC game, a lot of fans who found it by way of the board game were upset and complained (I know, shocking on the internet ). This led to arguments of Classic AP versus Persistent APs (all over board game geek iirc and some here) and imo lower initial sales than the game should have garnered.
Personally I came to the PC game from the board game but I didn't mind Persistent APs; it had its merits. If I had been asked, and there could have only been one mode, I would have preferred and recommended Classic AP, not splitting the community alone would have be reason enough in my opinion. However I like have both options available so in the long run, I think it's going to work out.
To finish the story, on their own dime and time, WCS (mainly Eric) put Classic APs back into the game but since there had been over a year of further development, it had to be reintegrated and tested. That's the last few months and all the patches, especially the betas. It also explains why the FFs are different from the Second Edition AtB and why there are some rule inconsistencies.
Regardless, WCS has done a bang-up job giving us Classic APs back and are close to stamping any remaining inconsistencies out.