Well, I've had some moderate success with getting the AI to create competent colonies but by approaching it a different way.
I reworked the AI_Facilities table to make the colonies a bit more general. I spaced out the Resource Generation facilities a bit and added in more Research. I also spread a few of the other two types of resource gen facs into each type to more or less 'hedge the bets' a bit. For example, a Refining Colony might have 3 refineries, 2 research and 2 mines. A Mining colony is closer to 6 mines, 2 research, 1 refinery, 1 farm. This way even if it is a dreadful planet for a specific resource, the planet is at least doing SOMETHING. Also, I deleted the 'Resource Storage' lines from the queue as well. It never seemed to use the stored resources anyways and the added production from more generation facilites seems to have made up for the lack anyways.
Also, note that the 'must have at least' line at the bottom of each entry seems to make it ignore any other restriction regarding percentage or planetary resource values. If you change the 'must have' number on resource gen colonies to 0, it sometimes has better luck.
As far as Intel...sorry, no help there. I cant even figure it all out myself let alone get the AI to do in correctly!

And I think its not really worth the space on the planets anyways. I've gone ahead and cranked up the number of intel points generated by each facility so that less are required in an effort to make them more useful, but I find that invariably, myself and my other players rarely bother with Intel. The AI seems to follow suit so no one is the worse for it at this point.
I'm hoping for a major rework of Intel in some future patch.
Hope it helps,
Talenn