I'm working with a blowfly genome (650M genome size). I have already used Ion Torrent PGM for sequencing but it only yielded about 2-3x coverage and around 4M usable reads (size select: 400, actually around 250, single end reads). I'm looking to sequence my samples on an Illumina platform but I don't know whether to use MiSeq or HiSeq. I am using the sequencing data to do de novo assembly (using CLCbio, V7) since there are no closely related genomes available (closest annotated genome would be Drosphila). Later on, I plan on using the assemblies to locate genes, microsatellites, transposable elements, etc.
What would be more useful: more coverage or longer reads? Any input would be great since I'm new to the bioinformatics field.