Well, first and foremost: timetabling.
The trains simply aren't run in any logical or sensible way, and I can give an example: it's impossible to return from Warsaw to Wrocław at night after 17:08 (EIP - Pendolino). On the other hand, there's a IC departure to Poznań at 19:22. There are so many pathologies in the timetabling that it's hard to know where to start.
Then there's the IC trains themselves. The overcrowding is unbearable at times, yet PKP IC stubbornly refuses to implement a reservation-only requirement during peak times. Yet, PKP IC is going towards a policy of having fixed formation trains, meaning that they're actually reducing the flexibility of the network. The specific nature of Polish tourism means that routes towards the seaside will be packed in summer, and routes towards the mountains will be packed in winter. Fixed formation trains aren't really a good option in this context, because for instance, you'll want to deploy more carriages on Warsaw-Wrocław-Jelenia Góra-Szklarska Poręba in winter, but then you don't need so many in the summer months.
Then there's my favourite absurdity in PL: above 130km/h, you either need ETCS or the cab must be double manned. PKP Intercity have shown absolutely no will to get this changed, even though it means that the new Poznań-Wrocław line runs at 130km/h rather than 160km/h despite the line and the trains being capable of it. It is unbelievably stupid on so many levels, especially as 160km/h running from Poznań-Leszno-Wrocław would be a convincing alternative to the car.
There are also issues with train fares themselves. PKP Intercity introduced a new system based on yield management, but the problem is that it's now possible for students to purchase tickets in advance for as little as 14.50PLN (about 3 quid) for Poznań-Wrocław journeys. The 50% discount for students is a political bribe, but again, there's no will to restrict the sale of such tickets at the busiest times (for instance, Friday afternoons away from major cities, Sunday afternoons towards major cities).
Unfortunately, PKP Intercity is run very much on the basis of politics and not on commercial reality. The end result is that you end up with things like sleeper trains taking ridiculous routes through the country at night, because local politicians need/demand direct sleeper train access to tourist destinations so they can brag about it.