[AllSeq]

But if we used Miseq v3 kit 150 cycle, that is 2x75 paired end (if I understood that correctly) then we will not lose alot of data because we are not sequncing more than the insert size. Problem one checked, right?

Since we are using v3 kits then I dont think so the 15GB will be a problem.

If you cut the read length down to 2x75, you won't get the full 15Gb. The 15Gb calculation comes from 25M reads * 2X300bp reads. 2X75bp reads will yield only ~3.8Gb. And that's not really enough to fully cover an exome (especially if a portion of those reads are off-target).