The question is based on false premises:
The Eastern European Plain is often claimed as the homeland of the Proto-Indo-Europeans. If this is where the seeds of European civilisation were first sown, why did it take so long to found cities here?
The Proto-Indo-Europeans, whereever they lived, did not sow the seeds of European civilization, they sowed the seeds of European culture, or at least of most European languages.
The seeds of European civilization were sown in Mesopotamia and Egypt and slowly spread in various directions from those places into other places. Eventually they spread into a few places in Europe, mostly around the Mediterranean Sea, and from those places to other places in Europe, and so on and so on. It took thousands of years for the building of cities to spread from Mesopotamia and Egypt into Europe and throughout Europe into the Eastern European Plain.
"Rome wasn't built in a day", as the saying goes. Building cities takes time, and that time is spent in often exhausting backbreaking physical labor. Why should many people who have other tasks they could do commit to building cities? Societies have to decide that building cities from scratch, or enlarging tiny villages into towns and later into cities, is worth the effort.
And first of all they have to even hear about the idea of building villages larger and larger into towns and then cities. And they have to learn sufficiently advanced agricultural practices to produce a surplus of food to support more farmers who convert more forests into farmland to support more farmers who convert more forest into farmland, etc., etc. to build up the agricultural surplus in a region to support city populations.
When half the people who were born died in the first few years of their lives, populations increased slowly, so it often took many centuries for the population of a region to increase enough that cities began to form.
So city building was the result of centuries or millennia of agricultural improvement and population growth. The necessary ideas and techniques for those processes were developed in many widely spread places and slowly spread around the world from where they originated to places farther and farther away, and arrive din more distant places centuries or millennia after they originated.
The Eastern European Plain was apparently not a place where many of those ideas and techniques originated, and apparently was far enough from regular contact with the places where those ideas and techniques originated that those ideas and techniques reached it a few centuries or millennia after reach other regions.
But of course the species Homo sapiens existed for hundreds of thousands of years before the beginning of agriculture leading to civilization, and might exist in a civilized society for hundreds of thousands more years, so a difference of a few centuries and millennia in when various regions became civilized is comparatively minor. A few hundred thousand years from now, a timeline of history will make the spread of civilization across the world seem almost instantaneous.