There have been a couple of reports about data quality for PCR sample preps vs PCRFree preps as well as reports of the NextSeq platform on seqanswers comparing it to HiSeq V3. There is also another report (Slideshare) comparing HiSeq V4 to HiSeq V3.
Overall, the trend in those reports is that the data quality is, in order of best to worst:
Illumina PCRFree > Illumina Nano PCR >> Other PCR sample preps
Sample prep is the biggest factor for data quality at the moment, then followed by instrument differences:
HiseqV4 PCRFree > HiseqV3 PCRFree > NextSeqV1 PCRFree
There is one sweet-spot for the NextSeq which was reported by Dale Yuzuki, who works for Thermo (Ion Torrent), which is the low price per 100M reads for 1x75bp runs in the NextSeq, which are commonly used in RNA tag counting experiments:
In terms of data management and analysis, the NextSeq is highly integrated with Illumina BaseSpace. From the design of the experiment, barcoding of the samples, uploading of the resulting read sets up to the cloud, and then running of analysis in BaseSpace apps and sharing the results with collaborators.
The HiSeq machines are gaining data integration, but it is not as seamless as the NextSeq at the moment (2014-11-28).
If you don't want to upload your datasets on the BaseSpace private cloud, you can use BaseSpace OnSite, which is reportedly as good for the NextSeq as it is for the HiSeq.
In terms of throughput, find the relevant information below:
A run on the HiSeq with V4 chemistry 2x125bp takes 6 days and produces between 0.9-1Tbp of data:
At 15-20x per lane, and 16 lanes per run, that's 8 WGS 30-40x 2-lane genomes every 6 days, and 8*50 = 400 WGS per year not running it on Sundays and 2 weeks holiday period.
For exomes, multiply the 400 WGS by 12, and it gives you 4800 WES per year.
If you do half and half WGS and WES, you can do 200 WGS and 2400 WES per year with a HiSeq using V4 chemistry.
For RNA profiling, multiply 400 by 24, and it gives you 9600 RNAseq per year.
If you can do 200 WGS, 1200 WES and 2400 RNAseq per year with a HiSeq using V4 chemistry.