Back when I commuted on PATCO, 12th/13th was usually the least terrible of the bunch—the end of the line was only busy at peak commute times, whereas 12th/13th and 9th/10th would get used a bit more (people going to Jeff, etc.).

As for the trains themselves, sitting up near the conductor's usually a good bet if you're feeling unsafe — but PATCO's usually pretty responsive if you reach out about issues, which might help, too.