Yes, Family Guy and Shrek are essentially the same machine, designed by the great Pat Lawlor. The reason for there being two games with an identical layout is probably because Family Guy is more geared towards the American market because (at the time) it had almost no presence on European television. Shrek on the other hand is very popular all over Europe. Stern did it before with Nascar (who knows Nascar in Europe?) and Formula One (very popular here).
I own a Family Guy and think it's a great game. After two years of owning it I decided to put the Shrek software in, just for fun. So I downloaded the Shrek software from the Stern website and programmed it into my game with the totally convenient usb stick and behold! I now own a Shrek too
Seriously, they ARE quite different games. FG is rude, obnoxious (but in a fun way); generally not for the weak-hearted - where Shrek is quite the contrary: kids will love it and parents will too.
I am one of the few who quite likes this concept. Use a design twice and slap different artwork/sound/music on them. Doubles the changes of a success! And for us collectors it's easy to have one game in your gameroom and switch (a la pinball 2000).
Now if only I could get a fully populated Shrek playfield plus backglass somewhere, I would be the happiest guy having two games instead of one for the same square footage -- uhm, square meters I mean ;-p