The reason this happens is because its time to retire older members of a fleet. This happens in ALL transportation industries. One thing that gives railfans a bad name (to the railroad companies) is the insistence that the old be new and that anything old shall never see the scrap heap.
What you guys seem to forget is that the MTA is trying to run as cost effectively as possible. Like private railroads, the MTA is improving its fleet with more safe, more reliable, more economical cars to carry passengers around the 4 boroughs (not counting Staten Island). Think about it this way, in 50 years, some kid is going to be doing the same thing about the modern replacements you dread to see coming.
Remember, The Railways are a business first, historical museum second. Thats whats great about programs like Trainz, or MSTS or any train simulator, those retired cars will live on in people's harddrives and such. Thus keeping the memory of these cars alive in your minds.
Just some words to consider...