Much information about the Interregnum can be found at TES Wiki: http://www.uesp.net/wiki/Lore:Interregnum
However it is important to realize that his period was vastly similar to our own "dark ages" in a sense that society and general intellectualism were in much decline. Due to this very little is known about this time period, and it is a wellspring for adaptability into a new IP. For more explicit info, this game should occur sometime between 2E 830 when the Aldmeri Dominion was formed and 2E 896 when Tiber Septim conquered Tamriel.
I will attempt to shed a little light on some of the core issues I have been seeing people have with the lore being "retconned" for TESO, beginning with the biggest: Factions.
The Daggerfall Covenant:
High Rock actually fared better than any other province during the Interregnum, lapsing back into a Kingdom and City States style of governance with the collapse of the central Empire with relative ease. Orsinium was actually annexed briefly during the Second Empire by the Akaviri Potentate, thus the Orcs dwelling within became citizens of the Empire. While Orsinium's status as a province did not last long after the end of the Second Empire, I believe it is valid to assume that due to this recent status, the Orsinium Orcs were actually fairly amicable towards the Redguard and Bretons at the time, thus supplying a valid reasoning for their forming a faction. As for the Redguards, during the Interregnum it is known that the Ra Gada (Redguards) lost their dominance of the territory of Hammerfell to the Na-Totambu (Yokudan Royalty), as such they would be willing to align themselves temporarily with High Rock and Orsinium to regain control of Hammerfell, The fall of the central empire created an atmosphere where these normally hostile groups have founded a mutually beneficial alliance.
The Ebonhart Pact:
At some point during this time-frame, the Dunmer have recently experienced an Akaviri Invasion, as well, the Tribunal are driven off from Red Mountain by a re-awakened Dagoth Ur who claims Red Mountain, this instability and uncertainty kind of lead the Tribunal to begin looking beyond their borders to assistance from outside (lest we not forget it was Vivec who approached Tiber Septim some years later with offers of peace). The Argonians during the initial phase of the Interregnum experienced the Knahaten Plague, which hit the southern provinces very hard yet the Argonians themselves were mostly immune to it. Due to this event, many non-Argonians blamed them for the spread of the plague (which may or may not be true), so racial tension with the southern provinces has drastically declined since then, making the Argonians even more hated. Since the Flu was predominantly localized in the south, the Dunmer and Nords were probably not affected, and since the Dunmer defer authority to the Tribunal, it is safe to assume the Tribune opted for a mutually beneficial pact. Skyrim during this time was more concerned with the potential rise of a new Cyrodiilic Empire, and was fighting to keep their province free from their rule, It is not inconceivable in this desperate time when new armies are marshaling, that the Nords would create a war pact with their neighbours in Morrowind whom due to their isolationist style were not an immediate threat to Skyrim.
The Aldmeri Dominion:
This faction needs little explanation, they are well established as having formed in the year 2E 830 by the Altmer and Bosmer creating what is known as the Thalmor to govern Valenwood. It is known that the Elsweyr Confederacy allied with the Aldmeri Dominion (as well as Maormer and some Reachmen) during the Tiber Septim Wars.
Feel free to add to, discuss, and debate the Lore of the Interregnum.