I think part of it is that frame drag is a much smaller percentage of a road position than a TT position. I think it was posted somewhere that Pantani’s Cd on his road bike was 0.31, and he was tiny. 0.31 for a TT rider is the kind of Cd for someone double Pantani’s size.
I also think it has to do with tactics. In general, you are in the peloton, except when climbing. And when climbing, aerodynamics becomes less important.
Beyond that, I think it is important to consider ride quality. An aero tube, in general, will have worse vertical compliance (too stiff) and lateral compliance (too soft) compared with a round or otherwise shaped tube. Carbon has changed all this to some extent, since you can modify ride quality with lay-up, but for a non-carbon bike, it is much harder.
Cost and manufacturing is another issue. Round tubes and round lugs are easy to make. Cutting and fitting round tubes to another round tube for welding is easy.
Aerowheels are becoming more present because they have a big effect on acceleration. Despite being, in some cases, marginally heavier, they accelerate through the air much faster. There are also lots of company already making aero wheels. I think you are seeing more riders on Mavic Cosmic Carbones vs. Mavic Kysiriums. But these are wheels that are already being made.
Making aeroframes, for some companies like Time that use a lugged construction method, could mean massive changes. Changes that might take a long time to pay off. And when you consider that many teams still consider a lot of this aero stuff to be bunk, it’s not really surprising. I don’t think the general road riding public wants it, team riders don’t really know enough, so there is not a real demand.
I think that is the great irony about SlowTwitch. You have, to some extent, people that justify equipment choices “because the pros do it,” yet many of those same people probably have read more on equipment selection that many of the pros. Look at Jan Ullrich riding the Xentis wheel backwards. On the one hand, people say that his mechanic should have been fired. On the other hand, you might think Jan should know which way his wheel ought to go.