Game Completion: Completed, with only a few optional things remaining.
Overall, this game is a solid entry in the Megaman series. It won't change the mind of someone who doesn't like the series, but it is very satisfying for a fan of the series.
The plot of this game is adequate. It is not a great piece of literature, but it has a few good characters and the plot suffices to explain the events of the game and maintain the player's interest. Certainly, focusing a lot of the game on the interesting characters of Prometheus and Pandora helped it a lot, since those two are very different from the typical enemies of the Megaman series. I guess here is a list of a few good things and a few bad things.
1) Legion and the Sage Trinity are a nice addition to the series, though it would have been better for consistency's sake if they were at least mentioned in the last game.
2) The main villain is interesting, though he probably could have had more presence in his role as a supposed ally before his big revelation that he was the evil mastermind.
3) The portrayal of Model W in ZX Advent is very different than in the last game in many ways, and this is not adequately explained. Of all the things that seem like plot holes, this is the only one that is problematic for me.
4) The idea behind the four Megamen fighting in the Game of Destiny is a good one, but it wasn't executed perfectly. Their motivations and goals were not presented clearly, and more importantly they did not have enough presence in the game. It would have helped a lot if they simply appeared in more scenes, and had clear objectives whenever they appeared. As it is, they seem more like common minions than a group of idealists fighting some Highlander-style battle for ultimate power.
5) The power of Model A is clearly based on Axl's abilities from Megaman X7 and X8, but the connection between Axl and Model A is obscured by a lot of unusual stuff, and it seems that a few potential plot threads tracing back to Megaman X8 are still unresolved. I suppose more might be explained later, but it just doesn't make a lot of clear sense. Oh well, I guess this is fairly typical for the Megaman series, actually.
6) Prometheus and Pandora are great characters, so much so that the one fight against them is not enough. Fighting them each at least once more would have been nice. I fact, it would have been better if there were battles against all of the other Megamen.
Finally, there is one last issue with the game's plot: Ashe's story does not make sense. It was a good idea to differentiate the two possible main characters, but in this case the plot, particularly concerning the character's main motivations, just make so much more sense with Grey than they do with Ashe that it significantly changes the enjoyability of the story. Even the villains have better dialog when talking with Grey.
On one final note, I really like the system of collecting different medals for defeating the Pseudoroids in specific ways. It is a fun challenge that makes me want to fight the bosses several times. I vastly prefer it to the system in Megaman ZX, which punished you for fighting intelligently against an opponent and did not really reward fighting a boss any time other than the first.