RNA-Seq is widely considered to be superior to most other technologies such as microarray hybridization. Advantages of RNA-Seq include:

• Ability to detect single nucleotide variations, novel transcripts, indels (small insertions and deletions), gene fusions, and other previously unknown variations that cannot be detected by other technologies.
• Ability to detect novel transcripts, SNPs, and other alterations from organisms with previously undetermined genomic sequences - not limited to known genomic sequences, unlike hybridization-based techniques that typically require species-specific probes.
• Higher specificity and sensitivity than microarrays, which enables researchers to identify a higher percentage of differentially expressed genes, particularly genes with low expression.  
• Lower background signal and no issues related to cross-hybridization or sub-standard hybridization, which typically affect microarray assays.
• Lower technical variation and higher levels of reproducibility.
• Discrete, digital sequencing read counts.
• Ability to quantify expression across a wider dynamic range.
• Data is quantifiable, unlike microarray data which is typically displayed as relative to other signals detected on the array.