The major problem with running parallel to the tracks is that from Powell Street and the Cordova diversion until Victoria Drive you're in mixed industrial. Placing a station there right now means you would have to travel through these areas to reach the station/your destination which at night isn't really pleasant and it's likely that redevelopment will not happen for quite a while. We only just started redeveloping along Hastings. You could however rough-in a section of guideway for a station around the powell/woodland intersection, just in case.
From Victoria Drive and along Wall Street (or commissioner street, with walkway access, much like Sapperton) however you shouldn't have too much trouble running elevated guideways (or even at grade if space permits) to Bridgeway Street, then tunneling under Highway 1 to turn and emerge by the rail bridge where then you can cross to North Vancouver. You can't run elevated down Dundas as everyone will have a fit but you shouldn't really need a station in Gastown due to the proximity of Stadium and Waterfront (but if you want one to serve a corner of the region, I don;t think it would be a problem to have a station near the Heatley/Alexander intersection)
What you lose in station choice ("should I go to Station x, or Broadway/Renfrew?") you gain in overall accessibility of rapid transit. Joyce station for example is several blocks away from Kingsway but people are still willing to travel to it.
Okay, so the red line and black dots are the Expo Line and its stations.
The green line is my proposed elevated line with the tunnel under Highway 1, the blue line is the option of running along Commissioner street. The yellow line is a VERY rough idea of a tunnel under Hastings. The pink dots represent rough station locations (or a location for a future station). The only key place that will need a very close proximity station will be the PNE.
I feel though that not running elevated around the harbour would be a real shame.