This is a project where I try to tie all of the universes together in a single timeline. This might take quite a few leaps from Canon but should work well overall. Sub-Universes are part of the larger universes, and we are only counting character universes for now, besides Splatoon which fits in the timeline perfectly. If you can fit in the other universes or provide a Canon source that makes more sense (something connecting LoZ to FE, a logical placement of Kid Icarus, uncluttering Modern Day, and determining which events occur in which timeline after the Zelda Split) in this timeline, go ahead but realize that I might disagree with you. Almost all of these era names are cool sounding names I made up, if there is a more interesting/logical name you can make up, discuss it on my talk page
The “Three Kingdoms Era” includes Mario, LoZ, and Fire Emblem. The Mushroom Kingdom is nearby Hyrule as the Running Man makes an appearance in Super Mario Sunshine. This connection is further cemented when Link makes an appearance in Mariokart 8 along with the track Hyrule Circuit. The Fire Emblem franchise, although having no concrete connections to either series, logically fits within this timeframe. Hyrule makes various technological advances using artifacts from old societies, creating technology akin to our modern infrastructure. All of these kingdoms eventually die off, their stories becoming mere legends later on.
The “Modern Day” era is closest in technology to our current day. The top fighters of the Modern Day include Little Mac, Ryu, and the Wii Fit Trainer. Other notable athletes include Duck Hunt and the Ice Climbers, due to the rise in the popularity of sports. Giygas will attempt to invade earth, but is defeated three times and gives up. The remnants of space technology from the invasion usher in a new age of innovation, with advances that were once thought to be unattainable.
This “Machine Era” begins in 20XX, when technology advances to the point where the first sentient AI, Mega Man, is created. Future creations include R.O.B. and the 2D Mr. Game & Watch. A science experiment, if it succeeds, will create the timeline of Xenoblade Chronicles, otherwise leading to the rest of the timeline and the two different “Space Age” possibilities.
The “Space Age” has two very distinct realms of possibility. The first first is that earth enters an eternal ice age and that the native residents are forced to leave. You see this earth in Kirby 64: The Crystal Shards. The human refugees end up in the Galactic Federation, location of the Metroid series. The other possibility is that humanity is forced backwards when Pokemon come into existence. They develop kingdoms and eventually reach their own modern day. The humans eventually become extinct along with Pokemon. Those who survive become Pikmin over the majority of the world. In a small, isolated area, squids reach levels of sentience akin and surpassing that of humans. They then found the city of inkopolis, where Splatoon takes place. Although both Star Fox and F-Zero take place in this era, their positions relative to the two aforementioned “Space Ages” is disputable.
Kid Icarus, Animal Crossing, Sonic, and Pac-Man’s locations on the timeline are uncertain, due to a lack of potential time connections to other universes.