The thing is, most of the elements you mentions as decidedly medieval are only pervasive in some periods, and rarely at the same time.
The pervasiveness of Church power in Germany was a direct attempt to undermine the (semi-)feudal powerbrokers of Germany. Canossa made that not work too well for the Emperors, in the end, but others (like Philippe Augustus in France) managed to tie both the Church and, through the Church the country, to the ruler.
In so doing, they shifted from a feudal system of every landholder for himself and everyone for his landholder to one where the monarch or Church took serious power.
The last vestiges of the feudal system took longer to die out, sure, but gunpowder cannon, which meant a monarch could bring a rebellious noble to heel in days instead of months-to-years, firmly ended it (of course in some cases the ones wielding the cannon were rich cities rather than monarchs, but the center still could dominate the outskirts through organisation and weaponry).