Okay, Tolmekian... you've got my attention.
. . .
Great theory, nevertheless.
Well, my short answer would be that if you don't like it, then don't do it! 
Of course it doesn't change the fundamental conditions of the game - victory by defeating the other majors. What it does is do away with what one poster, whose name I don't remember, called immersion breaking comic relief minors (nasty little space squirrels, seriously?) and replace them with some more respectable - but still minor - opponents.
The longer, more thought out answer would be that you have valid points. My little quick-n-dirty guide didn't get into some of the finer points, but just gave the bare essentials to get minors to stop being idiots. A more lengthy guide would get into the pitfalls of modifying the minors. You have to take into account that the game treats minors fundamentally differently, then find a happy point where the minors can be more significant but not overpowered. Some key things:
- The intention is to make the minors more significant, but not to make them into 8 more majors. That's just a bad idea. The big problem, that you mentioned, is that they are exempt from the entire influence game. Their planets can't be flipped. Another, biger problem is that they don't count for victory conditions. So, if the super-minors wipe out the last major, then you end up winning even if there is still an epic struggle between you and the remaining minors, or even if you have only 1 planet while the 8 minors rule the galaxy.
- For the reason above, minors really shouldn't be given Super Abilities. Like Galacticdoom said, imagine a minor with Super Organizer. Now, imagine that same minor that is completely immune to influence. So the only way to take their planets is by force, getting attacked by all others of the same alignment. Yuck. Super Abilities just don't suit the minors. Not having Super Abilities is part of what seperates minors from majors.
- Minors get no customization points and almost no race bonuses. Another thing that seperates minors from majors. With the exception of the Akilians, the only bonus minors get is +100% to economics. That's a big bonus. In my mod, I take that away. No free money for them. I don't think they start with as much money as the majors, either. Coupled with the fact that minors only start with 1b population, they quickly hit economic trouble during the rush. They also only have 4 logistics points. Not so good. So, take away their +100 economics bonus and take away the Akilians military bonuses and the minors are quite weak. They'll expand, but neither as quickly nor extensively as the majors.
So, what I'm doing is giving the minors a normal personality, full CPU usage, and full economic resources (no bonus, no penalty), while leaving them without any Super Abilities or race bonuses. Seems fair. In fact, I'm playing my first suicidal game right now. Of the 3 minors I've met, 2 have 2 planets, and 1 has 1 planet. Another one has already been conquered. The rest of us have from 15 to 30 planets. Certainly not very powerful.
Now, I not sure minors are affected by the difficulty, i.e. they don't get the same bonuses as the other AIs at high levels, so they may do better on lower difficulties. They may not get the penalties at low difficulty levels, either, so they'd be more viable in that environment. Anyone playing anything less than tough probably shouldn't be fiddling around with the raceconfing anyway, though.
