Lets take everything into account piece by piece.
Donkey Kong for the SNES had some decent beats in it, I still remember the opening theme and krankies hut. But the music was used constantly for each level in each new part of the island except for caves which all had the same tune, and underwater which all had the same tune. it got on my nerves after maybe the second part of the island.
Chrono Trigger probably has one of the most beautiful soundtrack ever developed by a game company. Although the maps sometimes used the same piece of music again, it doesn't compare to what Donkey Kong had. Plus I never minded hearing Chrono triggers music multiple times.
Music goes to: Chrono Trigger.
In Chrono Trigger the graphics for the characters were in depth, 2D, and gave the characters some pretty sexy dance moves (Millenium fair and Ayla's party back in 600000 B.C.). The characters graphics changed enough to make you see how the emotion of the game and the story got to them as well as the music hitting in the right spot. The overall design of levels in this game is probably one of the best I've ever played in. The Level design and the depth that you can see in the graphics makes this one of the best games for the SNES.
In Donkey Kong however made 2D come alive with 16bit 2D/3D characters and enemies and well as stages. The way that Rare was able to take 2D to a whole new level by making these designs in a game is outstanding! The way the Characters moved made me feel as if I was using a real character. The levels, like the characters, were a 2D/3D side scroller that could possibly compare to the likes of the older marios. The graphics in this game being of a new age of fesign and playability have me wowed.
Graphics goes to: Donkey Kong.
Chrono Triggers story has depth, emotion, and everything else a good RPG needs to be a smash hit! Time traveling is a new concept in games when CT came out it was probably the first game on the market to have this feature. The character development and their back stories were excellent better then most games on the market today who's only goal is to make a pretty game.
Donkey Kong was about a monkey searching for his lost banana's... Do I really have to say more?
Story goes to: Chrono Trigger.
Overall winner: Chrono Trigger.
P.S. Chrono Trigger was followed up by Chrono Cross on the PS1. They started developing Chrono Break but wanted to use all the original staff on the CT project to make it. But now most of the staff working on the FF11 staff they aren't continuing it until they can get them all back.
P.P.S. I study a lot of gaming in my spare time. :P