Desmond may not be the strongest assassin, but he definitely has the potential to be the strongest assassin. It depends solely on how you look at it. For any craft or art that requires skill, newer generations are exposed to the knowledge of the past. For instance, if I had a master assassin as my teacher, it's safe to say that his potential will inspire me to reach his level of skill. Even after his passing, I'll be able to improve. If I then inspire my student to be as strong as me, he will have the potential to be as good as me, even better. And so on . . .
Clearly, Desmond's ancestors had started off as newbs at some point. Skill isn't inherited, it can be learned through practice. Although Altair was a master assassin and had the strongest sense of commitment towards his art, his skill was limited to his time. Therefore, Ezio (granted the art of killing passes on through time as it did) would have access to Altair's technique and moves, while Altair wouldn't have access to the know-how of using a hidden gun. Like I said, it depends on how you look at it. If you want to be technical, Ezio was a late bloomer and didn't exactly have the art of killing down to a science. Still, idealistically, Ezio has the potential to be as good as Altair, and Ezio's descendants have the potential to be as good as him. The only thing that changes throughout this progression is the technology, which would provide newer generations with newer skills and techniques.
I understand what Doon is arguing, but future generations will always be superior to a more archaic generation. Even if a descendant isn't as good as their ancestor, the actual art or craft has improved over the span of time, and thus those willing to learn the art, have an advantage.
Now all of this put aside for a moment, Desmond has a very unfair advantage above all of the other assassins in his bloodline. The Bleeding Effect will allow him to learn the skills of an assassin overnight. Absolutely ridiculous how far he has come in such a short time. He can use Eagle Vision, he can leap around like an assassin, he can brawl, and he can use the hidden blade. He's not far off now from being the ultimate assassin.