I can't comment on the 1968 team. I would say that the 2008 team was tactically smarter and more versatile than the 1999 team and much stronger defensively plus I think the squad had better depth, while the 1999 team definitely had the better midfield, was insanely strong mentally and was more swash-buckling.
Looking at Utd from 2006-2009, in 2006/2007 they very cavalier and played some truly dazzling football, and 2008/2009 they were more 'mechanical' and (obviously there were stand out performances such as vs. Chelsea at Old Trafford and away to Arsenal in the CL), while in 2007/2008 they were somewhere in the middle and the balance seemed to be just right.
I would say that Utd faced tougher competition in the Premier League in 2007/2008 compared to 1998/1999, but tougher competition in the Champions League in 1998/1999 compared to 2007/2008.