My list of cities that I'd love to see rebuilt:
London - western connector to M4 needed, so that you can enter and exit in all directions. I would also eliminate the crossover roads in North London, totally unnecessary. Also possibly extend southern entrance south as the M23 and connect it with the south coast
Dover - city is fine, but simplify the entrance to the Channel Tunnel from the M2/A2! Strange to take a country road and then backtrack... perhaps an M20 would be simpler?
Ruhr area, Germany - 4 cities of Köln, Düsseldorf, Duisburg and Dortmund should be connected more accurately, not just with country roads
Brussels (probably in the works) - the Ring needs to look like a ring and not a straight line! In fact most of Dutch-speaking Belgium needs work, already described in the relevant thread
Stockholm (planned anyway) - in the current map the city doesn't resemble Stockholm much at all
Copenhagen - ditto, plus the arterial road layout within the city makes it take unnecessarily long to get to and from the warehouses and the E20
Amsterdam (I believe MandelSoft has already done this but it's not released yet) - level junctions need to be eliminated from A10
Rotterdam (I believe MandelSoft has already done this too, but again it's not released yet) - ditto, level junctions need to be eliminated
Paris (I assume Kutchek has already made this better while working on France) - just needs to be completed, really
Some ideas, anyway... not really new ideas
but things I'd like to see.