Come on... I don't have all day!
So what do Pirates! and SimCity have to do with the disappearance of TB games? Well, think about it. You have only so many gamers out there. Each gamer can afford, on average, only so many games per year. Their collective spending power defines the size of the industry. If gamers spend $500 million on PC games in a year, then only $500 million can be used to pay for game development, publishing expenses, marketing expenses and tech support.
That's right - the money you pay for the games you play, pays for development of the next round of games. Pretty obvious, but it sometimes helps if it's explained. Say a publisher sees that a certain kind of game just doesn't sell anymore. For some reason, gamers as a whole have lost interest and are moving on to something else. Thus, the publisher stops offering contracts to developers to make that kind of game. Obviously, we're talking about turn-based games. As real-time games like Pirates! and SimCity became more popular, then TB games lost popularity - after all, the gamer doesn't have infinite funds, so he buys only the games he likes. He likes new ideas (to a point), so he tries these new-fangled real-time games. As the money gets spent on real-time games and not turn-based ones, the publisher focuses on making more real-time games, leaving a poorer selection of TB for the gamer, so he spends even less money on the genre.
The problem spills over
However, the problem gets a bit more insidious than that. Not only are publishers hesitant to fund unpopular game types (as they don't generate revenue), the developers themselves see this as a market that is drying up. This means that they spend little to no effort considering the market. They don't use their time to think up how they might make the next Civilization, how they might improve on Master of Orion or how to make an X-Com killer. Even if a small group of employees thinks up something cool, they will most likely be overridden by management - which is a lot closer to the money issues and is more conservative, trying to preserve the company. Or, if a new group of people get together to form a development house and come up with an idea, their complete lack of a track record (which very well might be considered worse than an unsuccessful track record) makes publishers hesitant to embrace this new development house - especially with their risky turn-based game idea.
Thus, since gamers discourage a genre by not buying those games, the publishers discourage development, and developers themselves stop working on ideas on the genre. The genre is now in a three-way vicious cycle: gamers won't buy the games because they see nothing interesting or new, publishers won't pay for the development of these games because gamers won't buy them, and developers won't come up with new ideas for the games because publishers won't fund development.
Follow the herd
One has to keep in mind that people, trends and fashion tend to move as massive waves. We have momentum. Something pulls us one way, we go until we've over-extended our reach, then go another way. It's a bit like a wave, but the motion is more than two ways. Right now, the real-time revolution is still going strong. Perhaps it won't ever stop.
After all, who would have thought that from Pirates! and SimCity we'd go to Dune II, Command & Conquer, WarCraft II, and then explode into a thousand other games. Among RTS games alone there are some true notables - Red Alert, StarCraft, Homeworld (and Homeworld: Cataclysm), Ground Control, 10Six, the Age of Empires series, Total Annihilation, Allegiance, Dark Reign, Dungeon Keeper... it goes on and on. This list is just real-time strategy games - it doesn't include RPGs or tactical combat.
Is there any genre that real-time can't supercede?
Real-time games have, over the past decade, taken over genres once dominated by turn-based play. The trend of real-time has, like that symbolic wave I conjured up, moved forward and forward, sweeping aside turn-based games. In certain cases - like CRPGs - it seems as if the move to real-time has saved the genre. Other scenarios, likes strategy gaming, simply have strong RTS games replacing strong turn-based strategy games.
At other times, the move is grudging and has even stalled - war-games are the perfect example. Though many a hardcore war-gamer would be happy with Gettysburg! or Fields of Glory, they hang on tenaciously to their turn-based, highly detailed and completely micromanaged turn-based classics. It's hard to imagine 360 Pacific's Gold-Juno-Sword or SSI's Western Front as a real-time game, yet maintaining all of the historic accuracy. Why? Well, consider this: the greatest generals at the time had huge staffs to help them deal with the army and make all the major and minor decisions a general had no time to deal with. How is one man and a computer supposed to handle that?
These war-games don't translate well to a real-time format, so they get ignored. The market for computer war-games isn't huge in the first place, so rather than risk development on uncertain projects, publishers simply focus on other markets.