In RS the stat experience system was replaced by the effort system, which basically works the same except:
-Stat experience is now called effort values (EVs)
-There is a cap on the TOTAL amount of EVs you can earn (510, which allows you to max out at most two stats)
-Lv 100 pokemon do not earn EVs even if they have not reached the cap
So the likely reason that Charizard isn't reaching the same stat level that it did in GSC is that its EVs are probably spread out among its stats instead of mostly going into HP, thus maxing it out. Now if you want to max out a particular stat, you'll need to train against pokemon that give points for that stat.