[Suicide Junkie]

3. Some of the research payoff versus cost seem unreasonable (especially in reactive armor). You can literally pay millions of RP to get a 10% improvement.

I don't have the authority to speak for the other things you mentioned, but I do have this one covered.

Don't for a minute expect to rush down the tech tree, straight for the top-end armor.
There are diminishing returns on all of these things, and in most cases you will never research right to the end. You do have the option but it may not be practical.

Most of the armor tech areas are optional, as well. You can work on the theoretical techs to achieve the ability to build emissive armor before you research refractive armor, for example.
At that point, you can ignore the practical refractive armor techs, and simply develop the more advanced emissive technology.

Skipping armor levels is a good way to save research points, but if an enemy appears at the wrong time, you may find yourself with a lot of theory, but no practical work completed, and your factories will be making expensive, low quality armor plates.

In summary:
Think "diminishing returns", and work towards the best tech levels you believe you can reach before the wars start.
There will always be higher tech levels to reach for. Anyone who gets to the top is just toying with his opponent, and pressing end turn a lot.