Wings of Liberty Plot Analysis: Covert missions

In this series of reviews I will be examining the plot of the various groups of missions in Starcraft 2: Wings of Liberty to highlight retcons, poor plots, and illogical decisions. Where relevant I will compare SC2 to SC1.

My main issues with the plot of Covert mission are:
1) That the first two missions are radically different from the last mission?
2) Why there's a choice when the player has no reason to trust Nova.

For more information about the problems with the plot of Wings of Liberty I recommend these threads:
http://sclegacy.com/site/editorials/7-reviews/1134-scl-reviews-wings-of-liberty
http://sclegacy.com/editorials/6-speculation/906-starcraft-retcons-analysis