Vostok? The same Vostok from AoKH and MFO? If so, welcome to SE4 (at least I havent SEEN you here before). On MFO/AoKH/Zone I was Imperious_Leadr....hmmm, maybe I shoulda kept that name for a SPACE game, eh?
Anyways, regarding your post...I had the same feeling regarding Organic and (to a lesser extent) Radioactives. My solution was to increase (rather greatly) the amount of Organics and Radioactives that Facilities take to build. The overall effect is that while you're colonizing heavily and building up your planets, you need ALOT more of these two underused resources. If you arent growing, you can afford to slack off on them.
Also, I increased the cost of the basic ship Hulls in terms of the Organics and Radioactives. IMO, this represents the food and 'fuel' expenditures for the ship (and, of course, its an ongoing cost due to the maintenance). Small Troops also have greatly increased Organics requirements (but less Minerals) as IMO, it represents the levying of larger number of grunts, again requiring more food.
The results have been very much to my liking. You definately cannot neglect these resources, especially early in the game when you are trying to heavily colonize. Later in the game, the ship maintenance guarantees that you have to make at least some investment in them to keep going. All in all, they went from nearly useless, to something I actively looked for good worlds to make use of.
The only real complication was the AI. Fortunately, with a little bit of playing around, I was able to get the AI players to build a pretty good, properly balanced, econ to account for the changes I made. So far so good.
Talenn