Okay, alot of these ideas have been mentioned in one way or another already, but I'll go through what I would like for EU4 (in no particular order... i apologise about the large amount of txt... rlly shows my passion for the game though

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1. No real-time battles (Like the Total War series). This distracts from the aim of the game, which is empire management and not tactical warfare. This would also stop alot of people on weaker PC's from playing the game. Besides, any attempts at that is doomed to failure, as PI does not have the budget the TW team has. They will simply be seen as a failed copy. Stick to your strengths. The TW series gives a great battle simulator with a crap campaign. EU gives a great campaign.
Do you really want to slap crap battles on there, at the expense of further development and enhancement of the EU campaign?
2. Stick with 3D. It looks fine, and most laptops and desktops should handle them fine. While a beautiful map is cool, the main thing is a functional, easy to read map. EU3 provides this, as does the Graphic Upgrade in MM. Though it is important to remeber that improvement can always be made. As the game gain popularity you might even start putting in unique grapics for each nation/culture.
3. Perhaps a statehood system, similar to Victoria/HoI3. With a policy of different states having different levels of exploitation. This would enable you to take non-culture territory, and then lower/increase their exploitation, in exchange for changes in stability cost, manpower, tax, pop growth, revolt risk and BB reduction. This system would likely require an increase in the number of provinces, to make all states at least 2-3 provinces big.
4. An improved economic system, where resources are actually consumed/required by your population and building. It could be integrated with the current CoT system so that a country can only buy resources from CoT's he has trade access to and that isn't blocked by hostile countries. If your country does not have access to a CoT, then it can't buy resources from provinces that sell their resources there. This would make each CoT it's own little economic area, with differing prices (depending in supply and demand) at that CoT.
As such, each province should only produce a certain amount of resources a month, to assist in this, with building requiring a certain amount to function (just so everyone got it). Buildings can include those that are required to train land and sea units (so that you might have the manpower, but if you can't supply them with the latest weapons/armour, then you might end up with inferior units or you might not be able to reinforce as rapidly). The economy would require the resources to actually circulate, instead of just dissapearing and appearing (obviously with stockpiles naturally declining if there gets to be too much food/wood/etc building up).
Thats pretty much it for the economic model (besides the inflation).... you get the picture, just more interaction from the player is needed really.
5. A better inflation system. The current one is lame. Saving up money should not cause your economy to inflate. Extreme levels of expenditure, unemployment, etc should. Inflation could be used to balance out research spending, where if too much is being spent on research, unit production (military maintenance), lack of resource for factories/pops, etc... then inflation rises. This would almost make much more sense than one that rewards you for spending all your money on everything but savings.
6. A stability system that doesn't just change when you get to a certain number. A system where it is a slider that moves depending on your countries performance. If your country is doing well, then the slider starts moving to the positive sidel. If your country is not doing so well, then it can start moving to the negative side. Events and the like could still affect it, by increasing/decreasing the stability by a fair bit in one go. Your countries performance can be measured by BB, Revolt Risk, number of cores to number of non-cores, portion of country that is state religion/culture, etc... I believe it would give a much more realistic portrayal, while also giving immediate (yet small benefits) to your country performing well, instead of waiting years and years for that stab increase.
7. An improved character system, with actual familiy lines. Sort of a mix of EU: Rome and CK. Where your royal family can marry and have heirs, etc... Generals and advisors (and other leaders in non-monarchy countries) can then be selected from these characters. There can then be succession wars and the like by actual characters, and you would have more influence over it. Personal Unions could still be formed if a leader dies without a heir, or the heir is a leader of another country, with this eventually leading to a inheritance or the two going to different heirs/chars later on. Different countries can have different succesion laws. Some characters could be restricted to a certain country.
Characters should be hireable by all countries that have that characters culture as an accepted culture (or if their nationality is from that country). All of these characters should have a gender, religion, culture (possibly the mothers culture), nationality (being which country thet where born in, this country being able to hire the character for cheaper) and political outlook (described below). All characters would also have stats (based off their DNA) which would grow with them as they fulfill different task, like being a general or an advisor. A system that is a good mix of the EU:R single country chars and the CK mulitnation chars.
8. A complete culture system overhaul should be done. Each province needs the ability to have more than one culture. This would be reperesented by different statistic and population numbers for each culture. This could be done almost like Victoria, where each pop was seperated depending on it's attributes, except that this can be done only by culture.
So a city may have three cultures, resuklting in three different pops to see and work with. Each of these cultures would then have statistic which show percentages of the cultures happines (revoltrisk), religions (with a higher state religion increasing the odds of a culture flip), language (as a french pop could start learning german when it's intergrated into a germanic country, with the language being the main decider in an eventual culture flip) and political outlook (total monarchist, constitutional monarchy, republican, theocrat, etc... This changing if a specific government is doing okay, with certain outlooks being more predominant in colonies or later in the game).
Populations should be able to migrate (slowly mind you) to neighbouring countries if those countries are doing condirably better than their own country, with the main movement being to provines that border their own cultural areas (adding a sense of cultural expansion). If a certain religion or political outlook does well in a neighbouring country, your pops may start wanting to adopt or convert to that. Rebels can then start adopting the policies of pop that they spawn from.
Pops may also need resources that boost their growth/happiness, with a lack of resources lowering their growth/hapines. This can also be reworked into the colonialism system. As we need migration from countries other than the colonisers to these palces. Not everyone in the British colonies was from England. The current system greatly inflates the population of one culture, over that of another, depending on how quickly it colonises.
9. Make it much more accessable to modders (even though it is already one of the most moddable games ever). I don't mod, so I don't know the limitations myself, but I do know that games like those made by PI can live or die depending on the input from the modding community, which help the game replayability (which is already quite high). Meaning, more modability always helps. I want this game to thrive, as it is 1,000 times better than the TW series. Used to love them, but I can't play them anymore. They just don't engage me as much as EU/HoI/Vicky does.
Anyway, that's my quickly thoiught out suggestions. Any arguments for/against any of these concepts are welcome, and very constructive. Us talking about concepts here, good or bad, could help the developers come up with good ideas of their own.
And I apologise if it seems like I'm trying to make this into a CK-EU3-EU:R-VIC hybrid, it's just that their all really good games on their own. By combining some of their concepts, we might hit gold.