Halo: how does the Flood make sense?

This is a very long question, so I will try to answer it as best I can and to the best of my knowledge.

I also want to add that I'm not 100% sure on this answer, but since nobody else answered you for over a year, I'll give it a go anyway!

"keep a portion of the populace alive in captivity and have them breed to ensure a good rate of growth

for some reason the Flood doesn't do that and happily consumes all life in the Galaxy until nothing is left"

My theory on this is simply that the Flood is a parasite, a disease, much like a cancer for example. Therefore, it doesn't have the mental capacity to perform such mass scale operations; it simply has one thing on its mind - devour everything.

"the flood are all telepaths. Or actually the Gravemind is

The Gravemind at some point is able to talk directly to Master Chief. Yet this ability isnt used anywhere"

I believe this might have been because the Gravemind was able to telepathically see that Master Chief's plan was to destroy the Halo ring anyway, thus essentially saving the flood (and everyone else in the galaxy), so he didn't need to control his mind... just a theory. Also, the Gravemind contacts Chief telepathically throughout a couple of missions in Halo 3, so this power is utilised somewhat.

"So why are the Flood this mess of "oh noes unstoppable virus with ultra-intelligence that consumes all!" but when it comes down to it the Flood's most basic principles of operation are dumb as a brick and they aren't as unstoppable a virus?"

I refer back to my first statement - that the flood are but a parasite - which does seem very overwhelming and unstoppable, but that doesn't mean they are intelligent and neither does the fact they have supernatural powers.

Hope this answers some of your question!