Why change a winning formula?
What is more fun than having a random prov being able to run 50% more mod tpa of yourself (just a few more professors to max out thief science) by nothing but luck? Yeah it feels kind of unfair, but ultimately the game is still playable isn't it. So maybe just add some mechanics to even things out. In the old days we had happiness, to a good number of players, it was expereienced as totally random, maybe reintroduce something like this, but make it really random. Then have happiness affect a wide range of modifiers, tpa / wpa / dpa / opa / be, the sky is the limit. Then just like with science, generate a happiness point at random, but unlike science this happiness point can have both a positive or negative effect, and it has to be assigned to some happiness category. And if you make it perfectly random, t will be fair, just like the scientist system.
Sadly, you still can get the short end of the proverbial stick. Still not fair. So let's give players a chance to fix things, let them buy happiness packs in the ingame store. Each packs holds x happiness points, again randomly distributed, both positive and negative, if you're lucky, you could buy a whole set of positive happiness points (if you're unlucky, you are stuck with negative happiness points, but **** happens, then you just have to compensate and buy more packs).
Of course, this would add a whole new mechanic, maybe it's a little too much. In that case, just add more randomness by random gc generation, strip anything that generates gc from te game and give each prov an automated ToG each day, (again you can sell ToG packs ingame), or maybe strip military training, randomize that instead (with army packs for sale, randmly giving soldiers, specs or elites!).
Disclaimer, because this
whole science system totally sucked all strategy out of utopia making the game a whole lot less fun to me i started playing some "free-to-play" android games which might have given me the inspiration for this suggestion. (I don't think this scientists system can be fixed, it's not only the randomness that makes it suck, it's also the lack of investment in science, most suggestions that fix both create an awkward hybrid between the original science system and this new one (scientist that generate science points, really?), so i'd say just get the old system back and tweak (not replace) that a little instead. while this whole scientists thing is called science it really has nothing to do with science as it used to be)