1. auto-select site location profile post-login
2. auto-start "synchronize" or "keep directory up-to-date" with pre-selected transfer settings post-login
Eventually, maybe there could be a whole host of things you could automatically invoke post-login and you could arrange them into a list that is executed by priority.
3. write INI file in real-time rather than writing it only on exit. I use multiple instances of WinSCP and am constantly losing settings that I change in one or the other. This would also prevent WinSCP from losing settings after a crash.