Credit for all information in this post goes to spiritofsword from DuelEvolution
This info was obtained by spiritofsword searching through the YO3 database. Italicized text is a direct quote from spiritofsword.
1. We know all of the remaining area in this game (Kaiba Corporation, Stadium, World Tournament Grounds, Satellite Plaza, Arcade, Blister’s Hideout, My Hideout).
Well almost….. There still seems to be 1 area missing. There are a total of 8 areas in the game and only 7 listed here. Since the info in the database is hard to read since there are no spaces between words, it could be that the data was read incorrectly and maybe “Satellite Plaza” is actually 2 separate places; “Satellite” and “Plaza”.
2. We know all of the menu (Edit Deck, Card Album, Rental, Card List, My Profile, D-Mail, Duel Log, Team, Friend List, Ignore List, Leaderboard, Booster Pass, Duel Option and Return to Title).
A lot of this is the same as YO2. New options are “Card Album”, “Rental”, “Card List” and “Leaderboard. Of course “Duel Pass” is changed to “Booster Pass”.
“Leaderboard” most likely refers to a chart showing the top scorers in Events and TP ranks.
“Rental” is not completely understood yet but it would seem that we will be able to “borrow” cards from other players. However there is still plenty unknowns as to how exactly it will work.
“Card List” is really a mystery at this point. My best guess is that it will have to do with the rental option. Maybe a list of the cards you have rented from others or cards others have rented from you.
“Card Album” will most likely be the same as most Yugioh handheld video games. Were you can view a virtual album of all the cards you have, with empty spaces were cards that you dont have belong. You can most likely sort and filter the cards to your liking.
3. 2 Unavailable Menu at Edit Deck screen is Change Protector and Change Regulations.
Finally a name to go with the buttons! “Change Protector” would give you an option to change the appearance of your face-down cards. Cards in your hand (from the opponents point of view), cards still in your deck, face-down spells, traps, and monsters will all be affected by this.
“Change Regulations” is another option clouded in mystery. Will you be able to alter the banlist? Play Traditional Format using banned cards? How would this work when playing online against other people?
4. You can create custom duel with handicap (select starting LP) + Wait Time per turn.
Custom Duels should be a fun addition to the game. Surely there will be plenty of ways to have fun with these options. Most likely when you set one of these Custom Duels, your name will show up in a different color indicating the duel you set is indeed a Custom one, and your opponent will probably be able to see the rules of your Custom duel before the duel request is sent.
5. Trade Card menu at the shop (Blister’s hideout) is give unwanted cards to Blister and receive a card back. (We don’t know much about it).
Does this mean that we will be able to trade in all of our old event loss cards like Boo Koo and Dancing Elf for stronger, more useful cards? Hopefully this feature will prove to be extremely helpful for those who have a ton of old worthless cards as well as useful to new players who keep spending Booster Points on packs and many multiples of cards they dont need/want. Of course this is something we should be careful with as the card we recieve will most likely be random. The type of card recieved will probably be based on the quantity/rarity of the cards traded in.
6. Rent System will be add for sure and you can see it on the cards menu it will show you a cards that Currently Borrow and Currently Loaned.
7. Team Menu will have more feature and have 3 type of Member (Event Leader, Sub Leader and member) + There is a team meeting point+team level up and exchange information with a team member (We don’t know anything about it).
Its good to see more team involvement in the game. It will be exciting to see exactly what these new features are and just how far the concept of a team will be taken in the new game. Especially since in YO2 they seemed to be a frivalous addition to the game with no real purpose.
8. It seem like this game will have some mini games.
Another interesting twist to the game. These mini games will undoubtedly be played in the “Arcade” area of the game. An interesting thing to note is that on the main screen of YO3, the bottom-most area of 8 main areas seems to have a Duel Terminal in it. This leads me to believe that this are will be the “Arcade”. This also makes it seem that the mini games will probably be the same as or similar to the games that one can play on Duel Terminals in real life. If this is true, may it also be possible to win the Duel Terminal exclusive cards as prizes in these mini games? If so does that mean it will cost BP to play these games?
9. More NPC character from YU-GI-OH Anime will be added in the future + you can still get an avatar item+cards from them.
Some of the avatars that were mentioned in the database/by spiritofsword include “Mai Valentine”, “Bandit Keith”, “Maximilion Pegasus”, “Syrus Truedsadle”, “Prof. Crowler”, “Leo”, “Luna”, “Crow Hogan”, “Carly Carmine”, “Kalin Kessler”, “Blister”, and “Zigzix”. Strangely Mai Valentine is mentioned but not Jim Cook or the Evil Jaden NPC that we know will also be released. Does this mean that there will also be more NPC’s that were not mentioned here?
10. More Title and Avatar Items will be add.
11. You can LV down in this game.
12. There is a rate system that you can rate an opponent (like yo1). (Maybe It’s some text left from YO1 it may not added into the game).
13. Old event and TP Ranking still going on and there is a new menu Leaderboard.
14. On Duel Log Menu you can play and manage it (don’t have any information yet).
spiritofsword covered a lot more in his post. if you would like to see the rest his original post is here

