I was quite happy with the lovely unit counters and lovely map in Thunder In The East. Not so happy with how the profusion of generic fort and supply markers made it all look during play. Yeesh, was the encirclement of Moscow a mess! How about selling faction-specific-colored markers for supply and forts, making the lines of engagement both more attractive, and easier to keep sorted out?
Also, I wouldn't mind more brightly colored timer markers. The eyebrow shape is fine, but these tired 66-year-old-eyes just aren't what they used to be. No numbers needed, just red-backed-orange, yellow-backed-green, and blue-backed-purple (if 5/6 is necessary).
Jay is right, Barbarossa is "rush hour" for out of supply markers, and the Improved position markers have greatly diminished in the rules with errata. I hope you're using the v1.1 rules book.