Here are my thoughts on some communities that might meet your needs. The 1/2 acre to acre lot size really narrows it down.

In Rancho Bernardo (92127) –

The large communities like Santaluz, Crosby, The Lakes, and Avaron have some homes that meet your criteria- all are fairly new.

Here are others –

IvyGate in 4S ranch – homes between 3000-5000 sq ft, $1-1.5 million, built around 2006.
Downsides – lots of distressed properties

Santa Fe Valley (Bel Etage, Salviati, Savenna) – average 4000 sq ft, low $1 million, built in early 2000’s.
Downsides – intersections for these communities lack traffic lights, which can be a real problem during busy times on Camino del sur.

Gables crossing – mostly single story homes, 4000-6000 sq ft, acre lots, start at $1.5 million, new homes available.
Downsides – homes are all very uniform, this monotony might account for the extremely slow rate of selling (price, too?)

If you have a little flexibility and can go to $1.6-1.7 million, then here’s a great neighborhood in Carmel Valley:

Fairbanks Highlands – 4000-6000 sq ft, built in early 2000’s, guard-gated
Downsides – higher HOA fee – I think around $400/month

I believe that Poway probably has homes that meet your criteria, but I am less familiar with this area.