Quoted from Rat_Tomago:2 players are more sought after because there is less to tinker with, more artwork in the backbox, they made less of them (more rare) and the back box is lighter to carry. 2 players go for slightly more money depending on the game.
I would agree that the reasons above are valid for those who actually prefer 2-player games. However, I have to question whether 2-player games are actually more sought after in general as I've never heard this expressed on a wide basis.
As far as which sells for more, out of curiosity, I performed an unscientific sampling of Boston Pinball's eBay sales results and found that in 7 of 10 of the first 2P/4P pairs that I thought of, the 4-player game actually had a higher average sales price.
FWIW here is the data (avg sales price/sales count):
Snow Derby $348/9
Snow Queen $406/3
Surfer $564/31
Surf Champ $769/81
Quick Draw $720/43
Fast Draw $531/35
Card Whiz $527/31
Royal Flush $680/90
Top Score $492/43
"300" $440/74
Big Brave $535/52
Big Indian $557/31
Lawman $449/19
Sheriff $726/6
Jumping Jack $532/58
Jack In The Box $504/47
Duotron $401/35
Magnotron $467/8
Big Shot $503/43
Hot Shot $529/37