So here are all the things you'll encounter if you're playing a linked version of Oracle of Ages.
Main Quest Differences
In the beginning of the game, you will start with 4 hearts instead of 3. You will also have the Wooden Sword (Impa gives you the Wooden Shield instead, eliminating the need to buy one). Also, Ralph and Nayru will say that a message was sent that you would arrive.
At various points in the game, the game will cut to a scene with Twinrova. Also, the "hooded figures" throughout the game will not appear, because we already know that they are Twinrova.
Maple will be riding a flying saucer instead of her usual broomstick, making her faster.
On Crescent Island, instead of getting your shovel back from a Tokay, you will see the Tokay running off and Rosa will give you your shovel, saying that she got it from the Tokay.
On your way to the Nuun Highlands, Impa will tell you that Zelda was captured and you will have to chase Vire into the Black Tower. A minigame reminiscent of the Donkey Kong arcade game occurs, where you must jump up the tower until you reach the top, where Vire will run off and you will rescue Zelda. Afterward, she will give you a Seed Ring that can be appraised for the Blue Joy Ring, which doubles the effect of every heart you pick up.
Bipin and Blossom's Son
Instead of seeing the kid as a baby, you will see him as a kid. After beating Spirit's Grave, you can talk to him and answer his question; depending on how you dealt with previous things in Oracle of Seasons, he will be one of three kinds of kid.
If you told Blossom to play with thim, he is a fairly typical-looking kid running around. He will ask you if you have a girlfriend or not. Say yes or no, but I personally always so no since the thought of Link having a girlfriend would shatter my view of life.
If you gave Blossom 50 or 150 rupees and told her to sing to him, he is a kid with glasses running away from you. He will ask you if you're strong or not. Say yes or no, but I personally always say yes, since um, I'm obviously strong if I can save the world. It's just common sense.
This last one I've actually never experienced, so bear with me. I read a Bipin and Blossom guide, so that's where this info is coming from. Apparently he's a curious and happy kid and you have to give Blossom 1 or 10 rupees and tell her to sing to him. He will ask you what came first, the chicken or the egg.
Also, talk to Blossom at the same time and she will ask you a series of questions. If you say yes to any of them, she'll stop asking you questions. If you say no, she'll go on the next question. First she will ask you if you were energetic as a kid. Then she will ask if you were quiet. Then she will ask you if you were weird (what the h*** is wrong with you, woman?).
Depending on what you decided for all of this business with him, you'll end up with the kid going into a certain career.
If he is a farmer, he will give you a Gasha Seed. It's a pretty lame prize, but whatever.
If he is a hero, he will ask you how he can be powerful or whatever. If you answer with Daily Training, he'll give you 100 rupees later, which is pretty good. If you say Natural Talent, he'll fill one of your hearts, which is pretty much the worst reward ever. If you say A Caring Heart, he will refill all your hearts, which is also incredibly lame. If you say that none of them are right, he'll give you a pathetic prize of a single rupee. Of all of these, Daily Training is by far the best.
This one I've never gotten myself, so once again, bear with me, as this is from a guide. If he is a singer, he will ask you what is more important, love or courage. It doesn't matter what you say, since the reward is the same. Every time you visit him, he will refill all your hearts, like a Fairy Fountain. This is a decent reward if you get hit a lot, but it's not necessarily worth it.
If he is a...I don't know what to call him, but he acts like stereotypical "cool" kid. He will ask you for money. If you give him 1 rupee, you will get the Master Sword. Psyche, you actually get nothing. If you give him 10, he will give you a Gasha Seed. If you give him 50, he will give you 200 rupees (obviously the best reward). If you give him 100, he will refill your Seed Satchel, which is really lame.
After completing Spirit's Grave, go three spaces north of said dungeon. Talk to the Ghini here and he/she/it will tell you a secret. Go to Oracle of Seasons and go to the southwest corner of the graveyard. Dig one square above the grave directly to the right of the one in the northwest corner. Go down the squares and talk to the Ghini, who will let you play a minigame. All you have to do is look at the Ghinis that appear and say if there are more red or blue ones. If you're colorblind, that sucks. After winning, you will win an extra Heart Container. The Ghini will also tell you a secret. In Oracle of Ages, go inside the Maku Tree and tell the code to Farore to receive the Heart Container in this game too.
On the way to the Mystery Seed tree, you will find a Deku that is singing a song called "Love, Love the Seed". It will tell you the second part, which is apparently just 5 random symbols (it's really the secret). Then go to Oracle of Seasons and go to the Natzu Prairie. Depending on which animal partner you have, the place you need to go may differ slightly. However, you need to find a cave with a Deku in it. If you tell the secret to it, it will ask you to fill up your Seed Satchel completely. If you're doing the Ricky version, you can kill the Buzzblobs around for some seeds, but otherwise you've got a long and tedious task ahead of you. Once you do, return to the cave and talk to the Deku. It will upgrade your Seed Satchel so that you can carry either 50 or 99 seeds (depending on whether or not you already have the other upgrade). It will tell you a secret. In Oracle of Ages, go inside the Maku Tree and tell the code to Farore to receive the Heart Container in this game too.
After completing the Wing Dungeon, go to the ruins of said dungeon in the present. A great fairy will be there. Talk to her and she will tell you a secret. Now go to Oracle of Seasons and go to the Temple of Seasons, in the main area where you get the Rod of Seasons. Go to the very back and access the secret room behind the waterfall (oh wow, original idea there) to find another fairy. Tell her the secret to get a Seed Ring. Appraise it and it will be revealed to be the Heart Ring L-1, which will steadily recover your health. You must be moving for it to be effective, however. You can bring this over to Oracle of Ages by using the Ring Secret.
After getting the Roc's Feather, go three squares south of the mermaid statue in Lynna Village in the past. Then go one square west and jump over the pit. Talk to the girl here and she will tell you a secret. Now go to Oracle of Seasons and go to the second floor of the Subrosian inn place that the Piratians were living in. Go to the second floor and talk to the Piratian that is still there. Tell him the secret and he will ask you to get 777 Ore Chunks. This is a really tedious thing, but you have to do it. Just dig a whole bunch until you have then. Keep in mind that he wants exactly 777, so if you have at least 768 Ore Chunks, don't grab any red ones. Afterward, he will allow you to carry more bombs and tell you a secret. In Oracle of Ages, go inside the Maku Tree and tell the secret to Farore to receive the bomb upgrade in this game too.
After completing the Wing Dungeon, go to Mayor Plen's house. A woman will be in here. Talk to her and she will ask you to tell Mayor Ruul a secret. Now go to Oracle of Seasons and enter Mayor Ruul's house. He will allow you to carry either 3 or 5 rings at a time, depending on whether or not you already got the other Ring Box upgrade. He will also tell you a secret. In Oracle of Ages, go inside the Maku Tree and tell the secret to Farore to receive the Ring Box upgrade in this game too.
Old Man Secret
After completing the Skull Dungeon, go to the Ember Seed tree south of Lynna City in the present. There will be an old woman there. Talk to her and she will tell you a secret. Now go to Oracle of Seasons and go to the Clock Shop in Horon Village. Dig one space above the top right corner of the building. A staircase should be uncovered. Go down to find an old man. Talk to him and tell him the secret. He will test you by having you fight several enemies. You have a limited amount of time to kill them all. If you succeed, he will upgrade your sword and tell you a secret. In Oracle of Ages, go inside the Maku Tree and tell the secret to Farore to receive the sword upgrade in this game too.