I've got a idea of my own for the Red fight that I think would be pretty great.
Picture this. You're traversing Mt. Silver as normal, and everything seems just as it was in GSC, aside from obviously the graphics. However the cave does use a different tileset to all the other caves of the game, something a little more navy in colour, and darker. You reach Red's room, with ambient lighting, and exotic orange stone. You walk over the naturally formed orange stone bridge, suspended over a great abyss, which has blackness at the bottom as you reach the end, you spot Red, but before you can talk to him, he flees up a stairway. You go up the stairway into a new room. This room is orange and well lit just like the previous, but it is more 3D, and you must traverse upwards through the room like some of the gyms which have depth based puzzles. You go up stairways, waterfalls and slopes to the top of this fancy new room, where one more stairway lies.
Up the stone stairs lies the peak of Mt. Silver, rainy, dark and foggy. Red is standing there, looking off of the peak into the storm and the clouds. Talk to him, and he gives you his trademark "... ...", commencing the battle. The battle is as it was in GSC (the storm was merely an atmospheric effect and it is not raining in the battle), but with slightly higher levels. Red's sprite is his FrLg design but in his GSC pose. The music playing is the GSC champion theme playing in a remixed style, or better, the original 8-bit tune.
Once you beat Red, he says nothing and vanishes into thin air, leaving you on the peak. The fog clears and the rain stops, revealing the whole mountain range in front of you. The camera then rotates around Gold/Soul like in the Magnet Train cutscene and you get to see an overhead view of both Kanto and Johto in 3D.
The credits roll, with a medley of all the themes of the game playing (which eventually turns into a remix of the GSC credits). The credits roll on the bottom screen, with the top screen being utilized to show angled shots of all the towns of Johto and Kanto, and other places of interest like an overhead of the Power Plant or Moo Moo Farm.