How Super Pokémon Mystery Dungeon should have ended:
So, Super Mystery Dungeon is supposed to be the "game to connect all the past games", and they kinda did with the small references, nods, and that little cameo of Xatu, but imo they could have taken it further than that. Picture this.
None of cameos / nods appeared in the game until you beat the main story. Dark Matter is destroyed, and your partner is back by your side, and you both go on to do your normal expeditions as always; until Swirlix and Buizel accidently break the Nexus map again. Ampharos says this is another big setback, but this time has an idea. He sends everyone out on a normal expedition, but sends you and your partner to go visit the "sister group" of the Expedition Society. He explains that because the world is split into many continents, that they setup multiple communities that help out discovering parts of the world, one of these communities is Wigglytuff's exploration guild in the Grass Continent. Your job is to go there, and get their maps that they made during their time of exploring. Here is the next chapter of the game, where your new home town (for the arc) is the guild. Wigglytuff said he would agree to give you and your partner their maps, but only if you help them out, which is where you go and help the current explorers there, ie. Sunflora, Bidoof, etc. Once you recruit and gain everyone's trust, Wigglytuff gives you their maps, and then tells you that he knows of another group in the Mist Continent, that also explore areas. He tells you to go to Post Town, and look for "Paradise".
This is where the next arc begins, where you sail over to the Mist Continent, and meet Emolga and Dunsparce. Emolga tells you and your partner that the owners of Paradise are away, and he is left in charge. You tell him why you are there, and he tells you that Paradise is a place built on trust, and to trust you, you will have to go around helping the people around Post Town. Swanna lends you a place in her Inn, and this is your "home town" for this arc. You go around, helping everyone until you recruit them all. Once you complete all the missions and get their maps, Umbreon says that he might know how to help you on your quest to build the Nexus map. He tells you and your partner of a famous Rescue Team in the Sand Continent, known as Team A.C.T, lead by the famous Alakazam, and says that he has been around that continent so much that there probably isn't a single place he hasn't been to.
So, you set sail to the Sand Continent and this is where the next arc begins. You arrive at Pokémon Square, and ask around, wondering how to find Team A.C.T. The villagers tell you that you don't find them, they find you. They are after all, a Gold Rank Rescue Team, and to get their attention, you need to make a name for yourself. In this arc you must go around, rescuing Pokémon like in the original game, until you yourself reach Gold Rank in Rescuing (not exploring). After you do, you notice a post left behind on the bulletin board by Team A.C.T, saying they are KO'd in some dungeon. You go and rescue them, which is when they admit their respect for you, and agree to share their maps to you.
After that, you head back home to the Water Continent, and rebuild the Nexus map, as your partner sheds a tear of joy, after seeing his dream come true. He turns to you, and thanks you for everything, but says that the journey isn't over. There are still Pokémon in danger, and with Mystery Dungeons, one is never quite sure what could happen...