Well, I've found some things that are used in Seasons in an Ages ROM. Here's a list of the graphics:
-Rod of Seasons (In-use only)
-Subrosians (even dancing)
-Link unconscious as Din finds him
-Link using the Roc's Cape
Those are all in Ages, and I'm sure there's many more. In the weapon graphics, I noticed there are blanks and stuff where Seasons graphics would/could be, like next to the Boomerang. There are a lot of weapons with a black background and white lines going through them. My guess is Black is Transparent and white is another background color, because some weapons don't show and they might use them.
So finally with graphics, something I discovered a while ago is the big font graphics (used in dialogue) appear to not be in the ROM. There is the small font, and Capcom, being the people they are, wrote some sort of code that stretches the characters into big ones. Though, each character has more than two colors, so that probably helps a lot with it.
Now the last mixed thing I found is Seasons-only NPCs that have full AI. These include the dragonflies, and little moths that the Level 3 boss spits out. This gets me thinking: Maybe Ages has the code in it for all bosses or weapons and Capcom just disabled and enabled some. But then I think again, weapons in Seasons have IDs that are used in Ages by something else, so the code would be overwritten. What do you think?
Here's some of the graphics I found and put together (It's really sloppy, but you can see the ones I was talking about earlier).

~Lin