Something that I really, really like about the IDW Sonic comics is the way they have used the cast of characters, often doing a much better work and displaying a better understanding than the current writers for the games. In particular, I like what they have done with Amy ever since her debut in issue #2 (though being fair, this improvement can be traced back to the post-reboot Archie comics before the publication was cancelled). I really enjoy how she has in a way matured, no longer being a gag character like in some of the games where her characterization suffered from being flanderized to a single trait at the expense of the rest of her character.
Something that comes a a welcome addition is her being the one character that does the duties of a leader in the Resistance, despite Knuckles still being referred as the commander... Something I never agreed with for reasons that have to do with his particular character/personality.
However, although many fans received Amy's characterization with a positive reception, there are also people who waste no opportunity to question Amy's role, even going as far as calling her a "Sally clone".
I personally think that Amy growing into a leader is a development that comes much more naturally to her than it ever did to Knuckles: When Amy was introduced in Sonic CD, she began her journey as being no different from the civilians who suffer the consequences of Eggman's plans and who need to be rescued by Sonic. This is very important IMO since later it will play a part in Amy's development and interaction with other characters.
Next in Sonic Adventure, Amy was, for the first time, placed in a situation where she had to take action on her own without depending on Sonic to come save her. As her story advanced, we could see Amy starting to display a heroic side of her, one that drive her into overcoming her own fears and limitations to help those that were in need like the little bird... Hey, much like how Amy was also a victim in CD that needed to be rescued.
In Sonic Heroes, Amy is now in charge of leading two characters (Cream and Big) on a mission to rescue their friends. I think this game did a neat job at showing how Amy's personality and charisma offered someone whom Cream and Big could depend on to lead them to a successful rescue. Through their quest, Amy cheers them up and maintains the morale of the team, once more showcasing her aptitudes as a natural leader.
I think that what makes Amy a leader character for the resistance is that because of her humble origin, the civilians can relate to her just as how Amy can also feel empathy for them and the hardships that the fillain Eggman makes them go through. You could say that Amy is living testament of how anyone can be a hero if they listen to their heart and have the courage to do something about it... To do the right thing.
When Amy leads, it's not all about just giving orders. She also look after the well being of those who follow her, providing them with understanding and moral support, like when Knuckkes starts blaming himself for Eggman's forces having taken over Angel Island, helping him see that it wasn't his fault... Something that reminds me also of one of the last Sonic Universe story arcs where Knuckles is starting to have doubts about whether he is a good guardian, his mind drifting towards the negative like the times it has been taken away, to which Amy reminds him of the positives, like how he never gives up and always recovers and brings back the ME to safety. I think Amy is the kind of leader that will do everything in her power to make sure that everyone reaches the goal, together as a team, never leaving anyone behind.
I think it's fair to recognize that Amy is a different kind of leader than Sally. She may not be the most brilliant tactician since she is still a kid who is learning as she goes, but she knows how to keep the team united, since her strength as a leader resides in her ability to bring out the best in everyone, from your everyday civvies, helping them realize that they are stronger and more brave than they ever thought (since Amy went through the same trials and can talk from her personal experience) by believing in them to boosting the morale in stronger heroes like Knuckles who may start doubting themselves.
Tl;dr version: Amy is basically a kid friendly version of John Connor in the form of a pink, cartoony gerbil. XP