Let's review the secret endings of both KHBBSFM and KH3DS. Remember that all the secret endings of all games have a meaningful tie to the next.
KHBBSFM:
1-shows up at the beginning, with sora on destiny islands, talking about KH1
0-shows up when Aqua finds Ansem the wise in the Realm of Darkness
Right after, it reverses the ending, going back to the point where Aqua was saved by Terra and Ven's Keyblades.
This is where it says "Zero Point", basically 0.5. Here you find Aqua running into Castle of Dreams.
You also see Mickey in the Realm of Darkness, which I'm pretty sure he's searching for Aqua.
The last part, you see Sora and Ven disappear.
"A fragmented passage"-along with "blank points", there are events that happened during KH1-2 that are important and were not shown before.
KH3DS:
"The Darkness Awakens"-Master Xehanort returns of course.
"The Light in the Darkness"-Aqua trapped in Realm of Darkness. With this and the hints given in KHBBSFX, i believe its clear that Mickey is going to search for Aqua. Wouldn't make sense for Kairi to rescue Aqua just cause Kairi is one of the targets of the Organization.
Donald and Goofy complain that Sora is running late. It could be that he left without saying a word to awaken Ventus, or that a memory of Roxas/Xion that he saw with his meeting with Roxas gave him a clue on how he can help them. It might be Ventus just because Ven was the final boss, and I think Ven is calling out to Sora and/or trying to lead him to where he is.
Lea is off at Radiant Gardens, not getting any training. I don't think he needs any keyblade training considering that he is an AWESOME fighter WITHOUT a Keyblade before. He's probably investigating Terranort's study, and maybe he'll find Aqua's keyblade and armor.
The Seven Lights that are suppose to face off against Organization XIII are Sora, Riku, Kairi, and Lea for sure. According to the ending of KH:Recoded, Mickey and Yensid know where Aqua is and they're close to finding Ventus. That's 6. While Terra status is unknown right now, Mickey is there. I believe that Terra is the 7th, and why? Mickey is a mouse , sorry.
Kairi shows up and is probably gonna be trained by Yen Sid, which is most logical. Mickey and Riku might help out with that too.
Regular Ending-Remember when Castle Oblivion was shown? Because of the camera quality, i couldn't tell if someone was walking towards the castle or not. If there was, it looked like Yen Sid by the color, but I really am not sure. Also, look closely at Ven. He raises his head!!!!!!! Did Riku defeating Sora release Ven's heart?!?!?
KH: Recoded
Namine said that Sora must awaken his memories in order to save everyone. A lot of memories returned to Sora in 3DS.
At the end of Recoded, Birth by Sleep, and 3DS, "Reconnect: Kingdom Hearts" appeared in all of them. I think Reconnect and Birth by Sleep Volume 2 is the same game, speaking about the events that took place behind the scenes during KH1 throught 2. I meant, is says reconnect, so reconnect them all together? yea... What happened to Aqua all this time? Did she find other worlds besides Castle of Dreams? What happened to Terra all this time ever since Xehanort split into 2. Why does Xemnas have some of Terra's memories (looking for Ven in Castle of Oblivion and hiding away Aqua's keyblade and armor)? Does Xemnas have Terra's heart without knowing it? What about Eraqus? Terra kept his hear just like how Sora kept Kairi's and Ven's. What's the whole time traveling thing with old Xehanort and young Xehanort thing?!?!?! Will Vanitas return? I doubt it . I think a Kingdom Hearts 0.5 (Reconnect/BBS Volume 2) is the new number, considering 3 is used in 3DS. I also don't think it will be KH3 next just because there's too much questions (and many new ones!!!!) left unanswered. A game that takes place from KH1 until the now would be great to answer it all!!!
The past will be reawakened as a new number
In never-before-seen detail
Prepare yourself for the awakening of the next number
Reconnect all the past games with Birth by Sleep Volume 2, also to me known as Kingdom Hearts 0.5