why do these programs have so many limitations

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Yes, it is a felony, but the plaintiff has to go through a lengthy and very costly process to do it. Since so many people do it, the MPAA prefers to harass the bittorrent servers. And most of the time, you get a warning before charges are pressed (so you can just stop then and nothing will happen). Once in a blue moon, they press charges (or typically charge a fine) against someone with a blazing T1 connection that uploaded a few terrabytes worth of data. You won't get in trouble if you have a normal 768k connection and you just like to download a few movies per month. I am no rookie bittorrent user. I know what I'm talking about.
 
I depends on who your ISP is.

Way back A dude in my Cisco class seeded BF2 and got a nasty C&D letter from his ISP, then he got dropped.

Some ISPs have packet sniffers that "sniff" out Torrent packets then thorttle down your Bandwidth.

Of course, there are Torrent encryption programs...
 
"why do these programs have so many limitations"
d00d, fer sur, i hate it wen i download +100GB of warez and my computer fcks up.