The Core 2 Duo E6700 is an old CPU. That was the high-end mainstream CPU in 2006. It's got a lower clock speed, lower bus speed, and overall is just slower.
The Pentium Dual-Core E6700 is a newer CPU, it was released last year (2010). Higher clock speed and FSB. The Core 2 Duo is only more expensive because it's hard to find, and it's an in-place upgrade for people with 2006 computers who don't want to change out motherboards.
For a new build, get the Pentium Dual-Core.