we are obviously talking about different things. the reason marvel 2 lasted so long was not because it was some crowning achievement of competitive fighting gaming. It's because it was one of the few 2D games available at all for half a decade when fighting games were barely being made and the fighting game genre was considered to be nearly dead by the public
The reason Marvel 2 lasted so long (compared to say 3rd Strike or CvS2, which as you may recall, were also out at the same time) was because the depth in the god tier (let alone the rest of the top 16). To this day, as I pointed out in my previous post, people are still finding out new strategies and tactics. The very same brokenness is what gave the game its life. Heck, the current god tier didn't even materialize until about halfway into the games competitive life. At the same time, there's speculation that, given another half decade, we could actually have a new god tier simply because the game hasn't been fully explored yet.
The problem is that you are looking at quantity and the percentage of the roster that's viable and frankly, this is a secondary concern. What really matters is the quality of the match ups.
A top tier of 4 is totally acceptable just as long as those 4 give us interesting match-ups, which was the case with MvC2. That game at the top was an arms race. Players would keep breaking the game and finding new stuff to use and abuse in the race to beat their fellow players. The "technology" has developed to the point where Justin Wong says that it takes about 2 years of just playing and learning to actually be considered competitive.
Finally, the whole "2D drought" is frankly, a myth. There were just about the same number of 2D fighters coming out then as there are now. Heck, companies like Arc, Examu and French Bread actually made their mark during this time. The only difference now is that there are more people playing.