In terms of character development and overall intelligence, I’d agree with you. However, in terms of math skills, Eli might be closer than you’d think. In time, he might even get closer in overall knowledge. Right now, he has a lot of potential, but hasn’t really had all that long to develop it. In contrast, when we met Sam and Rodney, they were already pretty well developed.
I imagine they would have tried to figure out the calculations for dialing the ninth chevron in house before bringing Rush in. When even Rush couldn’t get it, they put it into the game and Eli figured it out, meaning in that focused area, he has probably already passed McKay.
Sort of the same way they brought in the paraplegic character to look at the FTL in Sabotage. Sam and Rodney are generalists. If you don’t know what you’re getting into, they’d be the best choices, but if you do know, it might be better to pick someone with a more focused skill set.