I'm not really convinced there is a problem with the AI the way it is. Yes, its imperfect - if your idea of perfection is an AI that will always pick the most logical and optimal journey. The problem with that is, its simply not a real representation of how people use public transport. Just like the AI, real people are often seemingly illogical, taking seemingly suboptimal routes, strange detours etc. Imagine you're a traffic planner in a big city, you're analysing someones usage, and you can see that everyday they travel from point A to point B in the morning, and point B to point A at night. The quickest, most comfortable route is a single tram journey. However, you notice that 1 day of the week the person uses the tram for one stop, before changing onto a bus, then another bus before going back onto the tram further down the line. It looks utterly bizarre, why would anyone do this? Well, what you don't know is that every Tuesday this person picks up a newspaper they order that they can only get at one particular newsagent in town. The detour takes them right past that newsagents. You, as a traffic planner, will never know this motivation, you just see a bizarre journey. Maybe you have a tourist, who for 3 days just gets on a tram, goes somewhere and then goes straight back to his hotel. One day 4 he takes a tram, then a bus, then a tram, then a bus, and another bus, and a tram before spending 5 minutes in a shop and repeating the whole journey in reverse. Crazy eh? Not really, its the last day of his holiday and he wants to explore a bit of the city. What better way than with a travelcard?
Big cities are chaotic, and public transport systems are too. Not every journey is perfect, for various reasons. People don't know the system so they make mistakes, people who change lines to travel part of a journey with their friends, if you can think of it, there will probably be someone, somewhere who will do it. The imperfections in the AI go some way to representing this kind of chaos. We see as much about our citizens as a traffic planner would in real life, we can't do surveys to find out why people use the system the way the do, so its up to us to fill in the gaps using our own imaginations. Try it, its fun.