Best as I can recall from reading here and there, here's the state of play. Our friendly resident train locomotor might be able to correct me on some of the below:
No major correcting needed, you pretty much hit the nail on the head. Your well-versed on all counts;
Milton - CP issues, rectified - unknown
Kitchener - ARL construction, rectified - 2015
Richmond Hill - equipment train deadheading from Willowbrook + need for service increases isn't nearly as high as the other lines. We should see 6 morning/afternoon trains once the outpost yard on Bethesda Road is completed.
Of all the branch lines, Stouffville will likely be the first to see increased frequency since the line is suppose to be signalized by spring. Barrie will be next, although there will be a lag because they won't start working on signalizing that line until they're finished such work on the Stouffville line. They probably chose to do the Stouffville line first simply because its much shorter than the Barrie and therefore improvements in service can be put into effect earlier. Like you noted, currently high speed passenger trains on OCS (non-signaled) mainline tracks are limited to 30 minute frequencies.
Although there is one run which is only 25 minutes after the previous one in the afternoon. I don't have confirmation on exactly why this is allowed but I'd imagine it has something to do with the fact that this one train operates on a different type of clearance(a work authority rather than proceed). Its far too technical to explain but basically you wouldn't be able to run all the trains with this without making everything overly complicated, so its a non-starter. Improvements in frequency will have to wait until the line is signalized.
Interestingly enough, its been suggested that Barrie will be the first to see all day service outside of the Lakeshore's in the form of a weekend service or so I've heard.
The ARL will be running MUs that are fully good to go on all tracks sans waiver.
I'm not so sure about this. From what I've been told, the plan is to have 2 tracks of used exclusively for the ARL service and the other 2 tracks for Kitchener GO service.
However, to start the service I've been told that only 3 tracks will be ready. So while 1 track will be for exclusive use of the ARL and another to be used exclusively by regular GO trains, the middle track will obviously have to service both types to accommodate passing. Perhaps this arrangement will only be allowed with speed restrictions and/or certain safety systems in place. Which is also why there wouldn't be any issues in the Union Station Rail Corridor.
For example, trains on non-signaled mainline tracks are limited to a maximum of 50mph from a 1/4 mile when approaching any switch until it is determined that the switch is lined properly. This is in case someone accidentally left the switch 'open' the train could stop before entering the other track/spur/siding/industrial lead, or enter into it at a slow speed and hopefully stop shortly thereafter before colliding into anything or running out of track. (A 10 coach Go train can make a complete stop from 50mph in about 1 train length i.e 920ft/0.17 miles using full or emergency brakes in most conditions).