In the song "Mine, Mine, Mine", the word "mine" is a pun on "mine" (as in, "this is mine") and "mine" (as in, mining for gold).
Very broadly, "Colors of the Wind" is essentially a poetic description of an actual type of religion many Native Americans practiced, Animism.
During Kekata's prophecy, after the images of the settlers transform into wolves, one of them circles Kokoum, and is later stopped by Powhatan. In terms of story, the wolf represents John and the events that happen when he is near the two warriors. First Kokoum dies in a skirmsh with John at the hands of Thomas, and then he took the bullet meant for Powhatan.
The sequel starts in winter. Not only does this give Pocahontas an excuse to sing a bittersweet song about how all things must change, but it insures that when John Rolfe first saw her, she's wearing her winter outfit. That way, he's properly shocked when he sees her wearing only (Jacobean era) underwear.
Thomas says that the Indians "headed North" when they took John Smith away. And Pocahontas later finds John's compass. Where does the arrow on a compass point to? The compass was pointing her to the place the execution was being held.
Coupled with Alternate Character Interpretation. Ratcliffe says that this trip is his last chance for glory in the English court. Which explains why he's so desperate to find gold. And leading the battle on the tribe...perhaps he felt that he could get away with not bringing gold home if he could brag about slaughtering a tribe. Or was he hoping to die 'heroically' in battle rather than go back to England empty handed and be disgraced?
Pocahontas suddenly being able to understand English. And the language barrier being apparently forgotten? Only Pocahontas is ever shown speaking and understanding English. When she speaks to him in front of Nakoma, it's never stated if Nakoma can understand what they're saying. However her reaction could be either a) the tone Pocahontas is using - she's speaking casually to one of the white men, or b) the fact that Pocahontas is speaking another language. Pocahontas gives no indication that she also understands Thomas at the end. She can tell he's trying to be sympathetic. The English also don't claim to have understood what Powhatan said at the execution - they know he called it off because he undid John's bonds and he and Pocahontas just hugged. In fact, Ratcliffe's paranoia that it's a trick might stem from the fact that he didn't understand what Powhatan said. John also gives no indication that he understood Powhatan at the end.
Before the sequel came out, it went something like this. At the end of the film, Ratcliffe is taken back to England to await punishment for high treason. The punishment for high treason at the time in England was Hanging, drawing and quartering.
The sequel actually makes things worse, as it's revealed that the King believed Ratcliffe's version of events. John Smith is subsequently accused of treason, so presumably the other settlers were too. That's why we don't see any of them in the sequel - Ratcliffe had them all hanged, just like he said he would!
Actually a good few of them stayed behind. Notice how Thomas and the other guy say "God speed, lad" as John is rowed out onto the ship. The majority stayed behind to populate Jamestown while those who went back only did so to transport Ratcliffe and John.
It's not enough that the movie totally didn't not do the research on the real story in a LOT of areas, but the fact remains that Pocahontas died a rather miserable death by small pox at a rather young age, far away from home after the events of Pocahontas II, and also that the situation of the indigenous Americans didn't get any better.
It gets worse once you realize that life for the settlers in Jamestown was awful. Jamestown sat on an island that had been abandoned by the indigenous population because it was so bad. The hunting was bad, the soil marshy, and there was a shortage of clean drinking water. The settlers arrived too late in the year to plant anything. Many died quickly from disease and starvation; the winter of 1609-1610 was known as "Starving Time" that left only 60 of the original 500 settlers alive. The whole situation for the first colonists got as bad as it did because they almost to a man acted greedier than this movie's villain. It took some rather inflexible leadership afterwards to keep Jamestown from becoming a historical footnote. Even then, Jamestown was gradually abandoned after the capital of Virginia was moved to Williamsburg in 1699. Jamestown fell into disrepair and the site was furthered damaged during The American Civil War. Today, the site exists as a living history museum and archaeological site.
In their defense, the Powhatan (and other Amerindians) did this too, though usually for different reasons and with less waste. Necessary Evil perhaps?
Earlier in the film when the settlers were boarding the Susan Constant, a rat sneaks aboard. Rats carry the plague which would have wiped some natives out.
Why must John be torn away from the love of his life and taken on a four-month voyage across the Atlantic in a rickety wooden ship? To be put into the hands of 17th century medicine, which thought disease was caused by humoral imbalances and leeches were the cure to everything.
Alternately there's a Time Skip between Ratcliffe telling James his story and John Rolfe actually arriving. The Queen simply says they have to wait for John Rolfe to return. He could either be about to leave or only just left. There could also have been another ship sent out, this one with maybe just people to populate Jamestown. John Rolfe's ship only was there to transport himself and Chief Powhatan. John Smith's "death" could have been common gossip for weeks before Ratcliffe went to James to tell the story personally.