Strokes - To be sure, she could hit the ball a ton, but neither of her strokes was flexible or adaptable enough to win on all surfaces. On grass for example, she had trouble handling low skidding balls and all the uneven bounces. Of course, I don't think it helped much that her chief competitor on that surface hit a very good slice backhand or a virtually flat forehand from a high trajectory. As long as the ball bounced waist-high or thereabouts, Monica was a deadly hitter of the ball, hence her amazing record on rebound-ace. Given any other kind of bounce, she was more or less a baseline retriever.
Fitness/Atleticism - As some of you mentioned, she wasn't a natural athlete. Her court coverage was predicated on good anticipation of the ball. Nowadays, players aren't disguising the direction of the ball any better (even worse I would say with all of these open stance shots), but they are hitting the ball harder to the open court. Even with Monica's remarkable anticipation, she's now finding that her anticipation can no longer compensate for her lack of sheer speed. Also, because she was no longer capable of overpowering her opponents in the mid- to late-90's, her endurance started to become more and more an issue.
Versatility - With those two-handed shots, Monica was always going to find it harder to be a good volleyer. Furthermore, she was always going to find it harder to hit the kind of shots that can come in handy from time to time - slice backhand, dropshots, lobs, etc.. Lacking these shots/options, she really had nothing to hurt you with if you could run down her shots and withstand her power. Given that more of today's players can do both, run down her shots and withstand her power, she often found that even if at her best she could win a set from today's elite player she didn't have the endurance to outlast the elite player in three sets.
Possibly overrated - She apparently took the game by storm, winning so many grand slam titles in a span of 3 years. As a result, she was instantly elevated to a stature that neither her game, her athleticism, nor the competition would have allowed to continue over the long run. And, as history has proven, exactly that has happened.
When you consider that she won most of her grand slam titles against players other than Graf, arguably the standard bearer all those years in terms of talent and athleticism, and that head to head throughout those years (taking into account both majors and regular tour events) Graf continued to best her, it is possible to infer that the media had handled Monica's ascension to the top of the rankings irresponsibly by dismissing Graf so quickly. So, Monica's lack of dominance upon her return and in subsequent years is really no surprise to those of us who hadn't bought into all the hype and just paid attention to the fundamentals of the game.
Had the media handled the whole situation more fairly between Graf and Seles, much like they are doing now between Federer and Roddick, then I think today there would be much less of a controversy over the slams that Graf won in Seles' absence. Much like Federer, Graf was the more athletically and technically gifted player, but the media found a way to look past all that in order to bask in Monica's aura.