If you ever visit Madrid again, I can say that buses and the metro usually work pretty well (they do get quite crowded at peak hours, but I guess that's the case everywhere) and you probably won't need to rely on Cercanías for typical "tourist" activities. If you're planning to travel between cities though, I'd be a bit wary of long-distance trains!

PS: Roads are becoming worse as well but I've seen worse abroad. Just wanted to point out that infrastructures in the country are decaying quite a bit in general.