Hello Kirk - I concur w/ Jim - I simply wouldn't accept any subflooring (plywood) less than 3/4", and I would further stipulate 1/4" (preferrably 3/8") underlayment before laying carpet. I will simply state - a finished floor thickness of only 5/8" inch would be a joke! And I also agree, since apparently the subfloor will not be all that beefed up, to specify 16" on centers for the I-joists. To check this, find the midpoint of the top flange of any joist (width/2) and place a mark - then do the same on the neighboring joist. Measure the distance between these two marks - that will tell you the on center (o.c.) spacing of the I-joists. Jim was also correct to recommend solid blocking between the joists. I did a quick read about wood I-joists on the net, and from what I gathered, they will still exhibit flexing, but this can be reduced with blocking. A lot of this depends on your builder - is he a hands on carpenter, leading the crew, or does he drive around to his sites all day, in a new pickup and carrying a briefcase. IMHO, the latter variety will cut every corner imaginable to add to his bottom line. 'Nuf said.
And to reiterate one last time, insist on construction glue being applied on top of the joist before the plywood is layed. Unless you are present during this phase, there is no way of knowing if this was indeed done, other than to find the empty "tubes" laying in the trash pile later. You need to tell the builder you expect to see these. Quite simply, there is either the right way or wrong way to frame a house. Again, best of luck ... Tom