I think this has more to do with the natural desire to complain about things - perfect is the enemy of good and all that. There are definitely a lot of issues,

I think this has more to do with the natural desire to complain about things - perfect is the enemy of good and all that. There are definitely a lot of issues, ranging from, as you say, the heterogeneity of German public transport to the flat-rate-but-still-somehow-discounted-for-employees pricing structure. But I suspect a lot of this will get worked out over time. But the foundation does seem to be pretty clear and universal - if you have this ticket for 49€ a month, you will be allowed on all RE/RB/S trains, plus buses and trams. This alone is a fantastic deal for a lot of people. On top of that, some states will have some extra offers or additional forms of public transport with extra rules, but if you need to worry about that, then you needed to worry about that before the ticket anyway.