The core program is free.
You are paying for the world content (quests, locations, armors, music, weapons, etc.) and skills.
Prophecies and Factions are not "older" games. They might be "older" content, but they are hardly inferior content. Not only that but I find them to be quite nicely filled with other players. And, if you hero/hench the game, the number of players is irrelevant anyway.
With regards to the fact that Prophecies only includes 6 professions instead of 8; this is a good argument for making Prophecies a bit cheaper (which it is at most retailers), but Prophecies also has a huge amount of game content. It remains the largest Guild Wars chapter by far with regards to missions, explorable areas, etc.
The design of Guild Wars was influenced by trading card games like Magic: The Gathering. Generally, Magic sets don't get cheaper with time. The "old" cards you buy are just as valuable for gameplay as newer cards.
So, I don't think it's that likely that you'll find older Guild Wars chapters in the "bargain bin" unless the store managers are just ignorant. You can also expect that NCSoft will not charge less than $49 for online keys regardless of the age of the chapter.
There's little incentive to charge less for older chapters. If you like Guild Wars enough to buy an older chapter, that's great. If you want to wait and buy a newer chapter, that's great, too... as long as you keep on buying