Perhaps I'm missing something, but I am interested in what behavior you expect from the app vs the behavior you are observing.
(I've used iBart a few times, but not in a few months and not to route trips in Oakland.)
Are you saying that your train arrives at 12th Street at noon and iBart tells you to board a train leaving 12th Street at 12:01? Would you prefer iBart tell you to board the next train? (Not sure about schedules, is that about 15 minutes later?)
Yeah, pretty much. The problem with all transit apps (including Google) is that they only consider x/y distances for estimating walking time. Getting yourself out of a 5-story hole in the ground to catch a surface bus, for example, may appear as a nearly-zero walk to the transit planner.
I don't know about SF and BART, but in NYC it's not just a matter of telling you to board the next train. Since there are multiple possible routes from A to B it may well be that needing to take the next train moves one route from optimal to suboptimal.
So yes, ideally the app would know that you can't walk a city block and two flights of steps in one minute and nix that as a transfer option. Bonus points if it told you which part of the train to get on to minimize the transfer time.
In Switzerland, train connections are optimised for minimising time and allow for distance between the platforms in question. It's stunningly efficient.
(Hope I'm understanding your question correctly. I'm not from Switzerland, but used their train system for a week a month ago.)
They have an excellent web site and app, first up. It allows you to set departure and destination, earliest departure time (if you don't want to leave before 10am, say) or latest arrival time (i.e., so you can make a flight), tweak routing and see every detail to the minute. You can get print-outs (if required) telling you what to do and when. The platforms for arrivals and departures are set rather than vague as in many other countries so you know exactly what's happening in advance.
I'm confident that they've worked nation-wide to coordinate arrivals and departures to ease passage for the absolute majority of people. Each train change is aware of the distance between platforms so that it might allow two minutes to cross platform to another train, or seven minutes if you need to move a bit further. You don't get stuck waiting for 30 minutes or have two minutes to cross six platforms. (We were travelling with an infant and a lot of luggage that meant changing trains was traumatic - in Switzerland, it was a dream.)
In one very handy sequence, we caught a series of two gondolas down a mountain, switched to a bus, then a train, then another train. Waiting time was barely there - it was brilliant. Trains seemed to leave shortly after you got to them, like the world was designed around you. People were joining or leaving on other routes too and seemed to have a similar experience.
I got the impression that popular routes were optimised to minimise walking distance between platforms, but could've been imagining that.
Another handy thing was that every platform access had stairs in one direction and a ramp in the other. The underground systems in London, Paris, etc were no where near as handy for people with luggage or prams, often not even having lifts for disabled access.
From what I've heard of Switzerland, the real key is the trains being exactly on time. Once you can guarantee that, it's easy to set a connection at exactly 4 minutes or something. OTOH, if your train arrival time is +/- 3 minutes, your connections are going to be too tight or excessive most of the time.
It just needs an update that a realistic transfer at some stations require N amount of time minimum between trains to account for walking between platforms. Although the only issue I have had this far is specifically at 12th
(I've used iBart a few times, but not in a few months and not to route trips in Oakland.)
Are you saying that your train arrives at 12th Street at noon and iBart tells you to board a train leaving 12th Street at 12:01? Would you prefer iBart tell you to board the next train? (Not sure about schedules, is that about 15 minutes later?)