My $0.02:
On average I'd take Aikman over Favre, however, I'd take 'peak' Favre over 'peak' Aikman if that makes any sense.
There was a 4 year period there when Holmgren was still there reigning in Favre where Favre was the clear cut most talented / dynamic player in the entire NFL and it wasn't even close:
- Won 3 consecutive NFL MVPs
- Where he was very careful with the ball and had an incredible TD/INT ratio (for the time period):
- 1994: 33 TDs, 14 Ints
- 1995: 38 TDs, 13 Ints
- 1996: 39 TDs, 13 Ints
- 1997: 35 TDs, 16 Ints
Haven't said that, the beginning and large portions of his later career where very uneven. The Mike Sherman years (post Holmgren and pre McCarthy) he did whatever the hell he wanted and in some of those years he was positively Eli Manning-like in turnovers.
It's probably a bit note-worthy that Favre didn't play with single other HOF player on offense in that timeframe in GB unlike Aikman although Sterling Sharpe was certainly HOF bound before he suffered his career ending injury.
Anyway, in summary when taking the whole career into account Aikman was better, however, Favre at his peak was simply incredible in a way that Aikman never was (or maybe just never had a chance to demonstrate like Favre).