This is because they made the mistake of giving you access to pretty much the entire map of Johto the moment you get Surf, and they didn't want anyone to face overleveled enemies. So everything around and after Ecruteak is like L17 or something. I remember the Dragon gym being significantly tougher though.
I don't think the Elite Four's levels are that outrageously low. My Pokemon were usually around their 40s as well when I'd get there (whereas they'd be in their 50s in RB) simply because there's less EXP to gain in GSC.
Kanto wasn't very well thought out though. All the trainers are weaker than the ones before Victory Road iirc...L27-L29 or something. That makes no sense considering you have to beat a L50 Dragonite to actually get there. The gym leaders are around Elite Four level too. HGSS kinda fixed this though.