RNA-Seq library construction challenges: the biases of RNA fragmentation vs cDNA fragmentation
Good question, a lot of this is still being figured out. Here's what's known so far:

Fragmentation methods based on restriction enzymes aren't random. 

Reverse-transcription performed with poly dT-oligomers, which bind to the 3' poly-A tails, is strongly biased towards 3’ end of transcripts. 

Reverse-transcription with random hexamers results in an under-representation of 3’ ends. This is from the reduced number of priming positions at which the reverse transcriptase enzyme can start cDNA synthesis.