Putting your marbles on an anchor character who has garbage incoming options is a poor strat that will be exploited by better players. Vergil can't survive a single combo (like Phoenix sitting on 5 bar can) and him unassisted and with low meter allows just about any character to beat him.
The best in the game is one that can win you matches without any prior resources and that is and always will be Zero. Vergil can easily be disrupted by a XF guard cancel but Zero laughs at that strat.
The way Schmidt was playing against Vergil is how people should be playing against him. He snapped in Dark Vergil after killing Wolverine and Vergil was helpless against the mix up, in more than 60% of that matches Vergil was not a factor. The match boiled down to the Wolverine Magneto match up.
Of course Vergil's strength is in that second slot because you are not putting all your marbles in one place and you are more flexible with your resource use and Vergil play. You get his assist, safe DHC, Spiral Swords DHC for damage and LVL2XF Vergil with a single assist. That is his most optimum placing in a team but he is competing with Doom in that slot usually (TAC infinite instead of SS DHC). Point Vergil is not as strong as point Zero, Viper, Wolverine, Magneto which is why no one important uses him at that slot (too many weaknesses as a point). To me the best character in the game needs to decide the game as a point character... not be a "back up" character down the order for support/anchor purposes. The point position in Marvel is the most coveted position in the game, you build your team around your point usually rarely around your anchor/level up character. If support position was more important then Doom would be the best character in the game because Hidden Missiles are broke and his TAC infinites are outrageous. Instead I give more precedence to point strength and in that Zero is the best character in the game.
Top 4 in the game is Zero, Viper, Magneto, Vergil. After that is debatable but I like Dante, Strider, Dormammu, Spencer, Doom, Wolverine, Nova, Ammy, Morrigan plus a few other characters after those 4. I think picking 2 characters form the top 4 and one support character from the next tier is essentially an automatic top tier team. It's super top tier if that support character ends up being Doom which is why I feel Doom is top 5 material. So essentially 2 characters from top 5 and some other character from the next list or better yet.... make a 3 man team out of the top 5 for full on top tier.