Pretty evenly matched in terms of strokes, but at his best I would give the slight edge to Djokovic on consistency. Agassi probably hit a slightly faster average groundstroke, but had less net clearance. Novak's consistent depth would give Andre problems because, although his half-volleys from the baseline were amazing, he did cough up short balls off that shot. Agassi dominated other baseliners by taking the ball early and running them from side to side, but he never faced anyone during his career that could move from side to side so well and so fast and then hit consistently deep and heavy shots from those positions as Djokovic. Novak, with greater topspin available to him on forehand, can also hit extreme angle counterattacks from wide positions, which caused Agassi problems against Fed. Andre was a great mover, but not particularly fast.
Finally, Novak has a much better serve.
Check out Agassi's recent barroom interview with Tennis Magazine's Steve Tignor, where Tignor asks him what he thinks of the game today, to which Agassi replies, "It's better." Lendl recently said more or less the same thing. The top 4 now could very well be the best four players, on level of play, that have ever played the game.