I don't think JPR was that bad of a GM as many people in Toronto made him out to be. He made a lot of solid under the radar moves and did put together some solid teams under a tight budget. He did go all out during the 2005/2006 offseason by trading for Glaus and Overbay and signing Burnett, Ryan and Molina, though they did not cripple the teams future/farm system as the AA trades did this offseason. However, one thing I did like about JPR was the under the radar moves he made which payed huge dividends (signing Frank Catalanotto, Scott Downs, Greg Myers, trading for Ted Lilly, trading for Scutaro, building cheap effective BP's almost every season etc.
I still think the 2008 team was the best the Jays put together. The rotation with Halladay, Burnett and if Marcum, McGowan stayed healthy for the full season was one of the best in my opinion. Offensively, the team struggled heavily and I was disappointed that the Jays never went out and acquired a big bat when they needed one.
As for deciding on which GM has been better, I still think we need to give AA some time. If this Jays team made the postseason, I'm sure everyone on here would choose AA hands down. Right now, in terms of baseball decisions I'd say I have liked JPR's moves better since he was able to find a lot of value out of the signings and trades he made (outside of the Ryan, Wells, and Rios contracts which would be his only faults -- though with Wells I'm sure he was pressured from Godfrey to sign him long term).