My first guess was Astroboy, but when I tried looking up all the series, I was not able to find any "giant robot pilot" among his allies. The robot boy was mostly naked, except for an underwear, which seems to fit Astroboy. Unlike the giant robot which was piloted by a man, the robot boy was human sized, like an actual boy.
I watched it on the TV before 2005, and the graphics looked quite like what you would expect from Japanese animation from between 1980 to 2000 (coloured and not 3D animated).
Some details from some episodes I remember:
- In one episode, the boy was reprogrammed by a villain, because of which he went against some innocent people inside a building; some journalists, or a broadcasting channel perhaps? He pointed some kind of laser pistol at one of them and told them something in the line of: "Run [name], or else I will kill you!". At some point during the episode, the giant robot piloted from the inside by the pilot came to try and stop him, so the robot boy started shooting the laser at him, which he had to dodge with a lot of trouble. One detail that I remember is, whenever the pilot spoke through the giant robot, his voice was toned down to sound low bass sound.
- One detail I remember about the giant robot: when the pilot disengaged, it would lower his chair from behind the robot I think, which leads to another episode I remember. In that episode, I think the robot was having a malfunction. When he lowered his chair to leave the robot, instead of keeping him in a sitting position, the chair moved back too much, because of which he ended up laying on his back on it. During that episode, the young robot boy had to deal with a giant monster on his own (which was out of his league). He also appeared on the TV channel, because some journalists were filming him getting beaten up by the monster. Eventually, the pilot with the giant robot came back to help him. But unlike the other episodes, the giant monster was several times bigger than the giant robot. They eventually managed to deal with the monster, although I don't remember how.
- In another episode, there was some kind of giant monster who was a collector of some kind. There were several glass tube containers, containing what I believe were vanquished opponents in stasis, and one of them was the giant robot. At some point, the robot boy managed to unlock all the glass tubes, and he started helping the giant robot away (most likely the pilot was too weak to move himself). In the mean time, the other monsters which were in their respective glass tubes started assaulting the "collector" simultaneously, as he bragged about taking them out one after another (I think he said : "Next!").