My take on why people end up liking Blair more than Serena after watching the show
Both have obviously done questionable things throughout the show, but Blair was portrayed with much more dept, the intentions and reasoning behind her actions were shown in time as they happened which in our minds somewhat justified her actions. They also added more layers to her character by those dream sequences in some episodes throughout the series, her being expressive of how she felt to Dorota also showed where she was coming from.
When it came to Serena, all we would get was a flashback of what happened when some kind of reminder from the past showed up, or a confession later while talking to someone, there weren't many scenes showing how she felt about things or her expressing her feelings more. She only showed some depth during her relationship with Dan in S1, her trying to change. She was a warm friend at times, especially when the drama didnt involve her, like with Chuck when his company was in trouble. She did love Eric, but that wasn't focused on much either in the later seasons.