Kids don't have to be dumb (we already had one incredibly stupid human companion with Daniel Witwicky) - but I agree that they don't all have to be Peter Parker-esque freakish geniuses either. Gets boring after a while. But hey, at least Rafael doesn't have superhuman strength as well (e.g. like when Chip Chase tore a floppy disk apart with his bare hands -- I' not sure if even Arnold Schwarzenegger could do that!)
But to be fair, there have been plenty of fairly average (i.e. not demonstrating 'super' intellectual or physical abilities) human companions of the Transformers. e.g.
+ Buster Witwicky
+ Sam Witwicky (a bit too average perhaps)
+ Spike Witwicky
+ Sparkplug Witwicky (comics only, cartoon Sparkplug was freakishly smart - being able to repair Cybertronians on par with Wheeljack and Ratchet. He even BUILT an Autobot shell once! How does someone this smart end up as an oil rig worker? Or a mechanic... or whatever the hell his job's meant to be)
+ Jesse
+ Minerva, Go Shuta, Cab, Cancer, Bullhorn and Wilder (aside from the powers given to them by their bracelets, they're ordinary humans - and of course they lost those powers after their Transtectors gained sentience)
+ Jan/Jean
+ Akira (ambiguous gender issues aside)
+ Onishi Yuuki (aka Koji)
+ Bradley "Rad" White, Carlos Lopez, Alexis Thi Dang, Billy and Fred.
+ Sally Jones, Misha
...etc etc.
Tru dat. There were humans in Beast Wars, but I don't think they were as "token" as in other Transformer series.