I'd just like to take the time to point out the following:
United Airlines's configuration on their 747-400s consists of 12F/52C/70W/240Y, which works out to a pitch of 31" in Y
Delta Airlines has 48C/42W/286Y, which allows for a pitch of anything between 31" and 33"
British Airways has 14F/70C/30W/185Y, again for 31" in Y
and lastly Thai Airways has 10F/40C/325Y, allowing for a pitch of up to 34" in Y
I'd like to note that each of the aforementioned airlines are (relatively) well regarded and respected legacy carriers, and also note that the highest total capacity for any of these configurations is only 375. Far less than AE's certified max of 660 for the 747-400. Even Air France, which has 436 seats on their 747s, does not come close to that number.
Now, your Lion Air example has 496 seats aboard their 747s, and as mentioned above only serves the Hajj flights to Jeddah. Corsair International, which holds the record for most seats on a commercial aircraft, has 582 on their 747-400s (though this is being lowered to only 532). It is more than worth noting that both Lion Air and Corsair, as well as other airlines like it, are low-cost airlines who use the 747 to serve high-density seasonal flights to charter and/or tourist destinations. They are not highly respected legacy air carriers.
Also, I'd like to point out that you, Mr. Amadeus, have 598 seats on your 747-400s. Just saying.
(side note: this information took me all of 10 minutes to Google and look up)
So, what have we learned here today? Airlines, as one member once told me, "waste a ton of space on their planes for seats". But if they did not, we would probably have good ol' Mike O'Leary's World Famous Straddle Seats on commercial aircraft worldwide!
Now the question becomes: What can we do to make our airlines "realistic". Well, officially, not much really. As I said before, the creation of "realistic" airlines depends entirely on the end user actively going out and more or less handicapping himself for the sake of realism. For example: Taking time and Googling actual airline configurations for use by his/her airlines. A task I've found to be not at all difficult nor time consuming. This is but one example of how we, as a community, can go out and make the game more "realistic" with minimal official changes by the staff at AE. But alas, as I've seen, a completely free market is never self regulating.