Ahh, EUI. How quick people are to forget their own history!
For what it’s worth I completely agree with the OP; the vast majority of players (myself included) start at the earliest possible start date to ‘get the most playing time available’, then quit after 200 years. Meaning most people’s game experiences are shaped by an unlikely medieval trio of Byzantium, Burgundy and Bohemia. It’s just wrong.
EU, to my mind, should be about the great European powers facing off over Europe, America, and eventually, the world. A 1399 start date leads to very poor balance, and makes the eventual emergence of what should be the game’s main themes increasingly unlikely.
The EUI 1492 start date gave you a unified France, a unified Spain, an England no longer fighting the 100 Years War, a Muscovy ready to form Russia from the ruins of the Mongols, a strong, Istanbul-centred Ottoman force, and an Austria poised to auto-inherit an empire. Bar Prussia and Holland, you had all your great powers up and ready to go (and that game only let you play a great power, none of this conquering the world with Ryukyu rubbish).
I can’t tell you what the absolute best start date would be, but it has to be somewhere between 1453 and 1540.
Actually, the best option should be a compromise solution
If the default date was set to something like 1492 (or the Demise of Burgundy, or the start of Hapsburg Spain, whichever is better to reflect the birth of the Balance of Power between the European Dynasties from the 16th Century to the French Revolution, which is what EU3 should focus on IMO), but the Earliest possible starting date could be as early as 1399 (or 1356, which would require a reworked China, to say the least), I'd imagine far more people will start with 1492, instead. Especially if the game was designed and balanced for a 1492 or 1453 scenario instead of a bizzaro ATL 1399.