- Track maintenance is horrendous, and it's public knowledge (not that it wasn't known before, it was just hidden)
- Many high-speed trains are now running much slower after the accident, and will continue to do so. Also, compensation for delays has been significantly reduced
- Some rather important routes (Madrid-Málaga, for example) still have no service after the accident
- The public train company (Renfe) is now setting up a bus company and openly saying that this is going to be very useful for years to come (wink wink)
- Cercanías is absolute garbage in most areas but especially in Madrid, with constant delays, broken trains, etc
- The pricing situation has improved with recent competitors (Ouigo, Iryo, etc) but it's often still laughable - I've been taking flights instead of trains when I travel there since they're much cheaper (and nowadays definitely much faster, given all the issues)
I could continue but I guess that's plenty. I'd say taking a train in Spain nowadays is an exercise of faith for many.