IMO this development is much improved by the second submission. I won't comment on the height change, because its not my thing and frankly I don't really care... at least there is still some variation.
What I will comment is the huge improvement to the site plan. First, they've removed the pointless pedestrian bridge, as well as the loading dock to the Standard Bread building. In place of these is a proper transit plaza and better integration with the MUP on the west side of the Trillium Line. This will greatly improve the street-level pedestrian experience at the station and in front of the development.
Second, they've separated the north tower from the rest of the development (it used to be connected by a lobby and strange terrace). In between the north tower and the rest of the development is another plaza that serves to better connect Loretta Avenue with the MUP and Gladstone Station. It also preserves the possibility of a future pedestrian bridge over the trench in-line with this plaza - as proposed by the 2014 draft CDP.
You'll also notice they've taken the podium of Tower 1 (the south tower) and kept it relatively consistent throughout Tower 2 and Tower 3. Unfortunately the windows of the south podium are a bit simpler and a little less aesthetically pleasing (the north podium still has fancy windows). Overall I'd say the podium and site plan are much improved - and that's what most people are going to see when using Gladstone Station.