On a project the size of Eglinton, having the LRT duck under major intersections along Eglinton East won't be a deal-breaker in terms of overall project cost, but it would definitely increase the efficiency of both the line and the traffic flow on cross streets.
Have the station at each major intersection be underground, but directly underneath the street, with the cross street providing a roof over the central section. The platform would extend out on each side, and then after exiting the station the track would ramp back up to at-grade, or near at-grade. When I get some free time I'm going to sketch up what I mean.
It would be a really bare bones station, with the northwest and southeast corners of the intersection both having a small structure with an elevator and a staircase leading down to a small mezzanine right beside the platform. Think Dundas Station, but less elaborate. The northeast and southwest sides would just be a simple staircase, like at the downtown stations. No heating required, because it would be mostly open air, with only the intersection above providing shelter.
Would it be more expensive? Yeah. Would it be a worthwhile expense? You bet your ass.