I'm with those wanting the lucky nations to go... in the long term. Ideally, the game wouldn't need such a crutch to resemble history. Now, I realize it would be impossible to create a game with mechanics using randomization which would then give today's world as a result at each playthrough.
However, I also feel lucky nations is cheating because the AI benefiting from it doesn't play with the same general rules than the other countries. At least in an oberve game, they definitely have an advantage. I would like the game to simulate better some historical circumstances instead of relying on such an arbitrary modifier as lucky nation. As someone said, France was populated and its power came from that. England was able to colonize most of the world because it was isolated on an island. France would thus have more manpower than others because some parts of its territory would be more populated (more BT) and England would have a bonus to colonist because its mainland has many coastline provinces. Giving bonuses linked to those kind of things would be acceptable railroading because it wouldn't feel forced on one tag or another. England would probably lose the bonus if it were to inherit France, but would gain France innate bonus because it would have conquered its territory. Spain crumbled because it became incredibly rich after conquering the Americas which were closer to it than for any other european country (except Portugal, which had its share of it but was smaller).
Not everything can have foreseeable causes, of course. The rise of Brandenburg is a common example. Yet, someone can argue that Poland had a flaw as soon as it allowed its kings to be voted by the aristocracy and selected within neighbours candidates. Still, this doesn't really explain how Prussia became an highly organized and militarized country. There could be some leads, however they would be more controversial than explications about France. Sweden involvment in the 30 years war and carving of a little baltic empire was also such an unforeseen event.
For those situations which could clearly be related to a general mechanic linked to the territory, the religion or the government type instead of the country, I would like much more for those general mechanic to be there and appropriately exploited by any AI finding itself in the situation than having to battle against an AI which would be unequal by design.
I remember when I first read EUIV DDs. I sulked the game during many months because I was angry about lucky nations and national ideas. In my opinion, this was wrong because it wasn't the existence of those countries which gave then advantages, but rather the advantages given by their situations (and sometimes luck) which built the countries as they were. I finally leapt forward and appreciated the game enough to want it to be upgraded, but I still think that, with a change : it would not be good to abandon lucky nations now and replace it by nothing. I think those situational bonuses I talked about should be gradually added while the lucky nations modifier would slowly become less important. Maybe it wouldn't be ever pulled out of the game, because some people like that if Brandenburg succeed and Saxony fail, but it shouldn't anyway stay in the same form. There should be other way than by military and MP bonuses to represent luck.