I agree the smaller civilizations could use a boost to make them more competitive. I'm not too bothered that they are harder to play though, I can see it as an alternative higher difficulty setting.
I do think giving the small states a boost can be justified though. Comparing the Netherlands to Canada for instance. In 1885 their populations were almost equal. (Canada 4.5mil, the Netherlands 4.2 million). While in the present scenario Canada gets 45 citizens versus 11 for the Netherlands. Problem is of course there's just not enough room in Europe.
So I think I'd try to give them other advantages (like giving them a bunch of wonders for instance, i think there are some mods around for more of those). Giving them great tile improvements like manufactories can also help and wouldn't be unrealistic i think. If scripting becomes an option, there are more possibilities ofc.
USA and Russia are also very strong in the game I'm playing now, I think it might be justified to reduce their amount of citizens. (in 1885, the USA had only a slightly bigger population than Germany for instance)