I think the key argument here is whether or not they are in the same mold; a semi-hip-hop/pop artist. But they aren't. They weren't even marketed the same. One, Beyonce was pushed to be the breakout star in a pop-group. Their sound was more in the Spice Girls wave than anything hip-hop. They weren't TLC, 702, they weren't even Total or SWV. Their music was never R&B Soul, or that "new jack swing/funk"; they were always meant to be Pop...you can make a case for "No, No, No" which didn't break until Wylcef touched it. Their appearances on Silkk the Shocker's albums was their attempt but they realized they weren't gonna make it there.
Aaliyah was marketed as a younger Mary J. Hip-hop beats with some ballads mixed in. Even now, Beyonce caters to the Pop crowd. Kelly tried to go the route more towards Soul but....Anyway, they aren't/weren't the same type of artist, so you can't really compare their music. Beyonce doesn't look for or cater to the hip-hop crowd. That's why Monica and Brandy made their way into this discussion. Beyonce has to be compared to Gaga or Amy Winehouse (even though Winehouse was more Soul sound), Madonna, Brittney Spears. Brittney was more her peer than Aaliyah