Depends where in CT you're coming from.

Hunterdon is a mostly rural county, unfortunately it's getting developed more and more. If you like the outdoors and don't care about night life then it's perfect. I've been here since 1987.

Clinton has the advantage in that it is at the confluence of rts 78, 22 and 31. There are a couple of local train stations and a bus station. However, shopping and dining are sparse. Want to go see a movie? Gotta drive 20 minutes to the nearest urb. We only have 1 supermarket and the Walmart is on the small size. On the other hand, several state parks are here, including Round Valley and Spruce Run Reservoirs, Voorhees state park, and several smaller parks. It still has a small town feel and is surrounded by a bunch of actually small towns.

Flemington is almost a city with tons of shopping. The hospital is down there. So is the main branch of the county library, although there is a major branch in Clinton.

Personally I prefer the Clinton area. My only caveat is don't buy near 78 or 31 otherwise you get to hear traffic, especially at night. Depends on the wind too. My neighbor likes to say we live in god's pocket here. Beautiful surroundings, not too crowded, peace and quiet, smells like flowers all summer, no extreme weather (except Sandy).

Hit me up with any questions you have.