A common problem of 4X games is that initial colony/city placement can often decide the game within the first fifty turns. This leads inevitably to a game strategy of frantically pumping out as many colony ships/settlers to grab all the best sites. This can get rather repetitive to say the least, is limiting strategically, and means unassailable leads can all too quickly build up.
The solution? Limit the number of colonies available according to the players logistics ability. Not only would each colony placement become more important lending a greater depth to colonisation, but this would make sense thematically as well - if logistics needs to be researched to shove a few ships together, surely it would be needed to co-ordinate a galaxy wide federation of planets, no?