Lag - old games generally ran smoothly on the old consoles, since:
A) The programs were much smaller and simpler (especially the graphics) and not nearly as much stuff needed to be done - The 2600 only pumped out graphics at 192 x 160 pixels, after all.
B) The programmers were acutely aware of what the system could do, and didn't try to stuff so much stuff into a game that it couldn't run - they generally programmed directly in machine language, and new how to write fast and efficient code.
The new systems running emulation rely on software, typically written in slower high level languages to simulate the execution of code. Much of the I/O in the Atari was very fast hardware-based - finding out the direction that the joystick was pressed was simply a matter of reading a single memory location, which also told you whether the fire button was pressed. Emulating this on a Pi or other computer will take much more effort, as the emulator will have to capture that memory call as a memory mapped I/O function and then fetch (through software routines) the appropriate data to populate the address - leading to control lag.
Mike
Edit - by smooth, I don't necessarily mean high frame rates - they generally just pumped out video at the nominal (NTSC) television rate of just under 30 frames per second. They tended to be pretty consistent though, without suddenly stuttering as the game loaded a bunch of textures, etc.