I had to get the flannel-lined jeans out of storage today. I only need them a few times each winter, but I'm glad I have them. If you spend a lot of time outdoors in the cold, I think long underwear makes more sense; if you're just walking to the bus stop or taking the dog out, the extra layer inside the pants does enough to block the wind and creates some additional warmth.
I thought about getting another pair, but the ones I have are fine and don't need replacing, even though I've had them for at least a decade, maybe longer. I got mine from L.L. Bean and what they are selling today is basically unchanged, except now they are offered in three fits and the pattern of the flannel changes every year or so. (This year's is rather ugly, but if you don't cuff them no one will see it.)
A couple of weeks ago I ordered a pair from Old Navy, just to see what they were like. The fit was just a little snug, though they were described as "relaxed fit." The denim was dyed a really dark blue, which seemed out of place, and there was a tag that indicated the dye could rub off on lighter-colored clothing and upholstery. Who needs that? The flannel was a red-and-black gingham pattern, which was fine, but the leg openings felt a little too narrow; there's no way they would have fit over boots.
I also have a pair of flannel-lined khakis, which I don't get as many opportunities to wear, but since it's going to stay so cold all week I may wear them just for some variety.