Basically, build up to the genius aspect, and not have him start as a jack of all trades genius, have him specialise in computer programming AND NOTHING ELSE. So in the pilot episodes he shows his natural talent by helping Ratchet troubleshoot the base computers, but he doesn't understand the alien beep boops of Bumblebee (I'd rather have Bumblebee talk than r2d2 signing but we already live in the worst timeline so rip).
The next thing he needs is conflict, which he had very little of besides the episode where he got grounded. Maybe build up to that a little more, we already had episodes where Jack had to juggle his life with autobots how about episodes where because he is learning how to talk cybertronian and how to beep boop with Bumblebee, that he starts getting ideas of being a language teacher or maybe coding edutainment video games. This conflicts with his parents who want him to be a straight-a doctor lawyer to support them in their old age. So he has to decide between his bromance with Bumblebee and his family, and he's a fucking little kid so obviously he has no idea how to cope and starts shutting down.
And the final ingredient is development, we started off nu-Raf as a repressed nerd who can't code cybertronian for shit but he sure as hell can make a minecraft-like in unity engine. By the end of S3 he's a little bit more confident in himself, manged to convince his parents to support his new aspiration of programming and language, and knows enough cybertronian to make that shitty little drone thing they used to find the nemesis with. Be sure to buy his dora the explorer-like edutainment games for your kids.
Its not an oscar-winning improvement but its better than his only shining moment being the time Megatron fucking beat his ass with one lazer shot lmao