If you go back maybe a few months ago in this thread, I also raised the concern that the OL will basically forever restrict the corridor to four tracks, instead of six, and six will be needed some day. However, I don't think limiting the corridor to four tracks is the end of the world. Four tracks is still more than the current three, it will save money in the short term for sure, and there are four track corridors like Berlin Stadtbahn that seem to work pretty well. When capacity starts becoming a problem, we could probably think about signal upgrades, platform extensions for longer trains, and maybe shifting VIA HFR to the Don Branch. And eventually, a downtown GO tunnel will probably be needed to relieve Union, so when that happens the east portal can be put just east of Pape to completely resolve the problem.
I also agree some of the station locations are not great, particularly the new Leslieville station. However, I think it's pretty reasonable to say that the fact that the stations are closer to ground level at least somewhat makes up for it. The above ground Eglinton terminus is also unfortunate, but given the lack of information we really don't know how bad the transfer will be (I don't have my hopes very high though - ML doesn't exactly have a stellar track record with convenient transfers). At least it will be a good transfer to the bus terminal though.
I also agree that the proposed station design at East Harbour is also very bad right now, but I that is really mostly to do with the lack of platform for the middle two tracks and less to do with the OL. East Harbour is empty right now and I see no good reason as to why we can't fit both OL and platforms for every GO track.
As for the northern section, what exactly are the concerns? Is it just tree removal? I'm genuinely curious.