My thoughts on the various NIs.
Quantity/Quality/Offensive/Defensive - No matter what, these will make up your land military picks. The only difference is which order you pick them up in, and largely dependent on what you need at the time. Defensive is a common first pick, because attrition is a massive early game troop killer and this makes you both take less attrition, and the enemy take attrition when attacking you. Offensive gives you discipline and buffs up your generals atac traits, Quantity lets you field a much larger army, as well as giving you a lot more manpower, Quality gives both discipline and infantry, cavalry, and artillery combat bonuses, as well as some combat bonuses to ships.
Aristocratic - Not a bad idea group... but its biggest downside is that it has to compete with the above four. If it was dip or adm, I can see it being picked a lot more.
Plutocratic - Good... but, same issue as Aristocratic, and on top of that is tied to a non-meta government form (republics)
Naval - Ehhh... if you want ships, go Martime/Quality, if you still want ships, maybe? Seems like overkill in most situations.
Administrative - Some people pick it for the one decent trick it can do, core creation cost, others pick it for the mercenary bonuses, I care for neither (Note: Core creation is awesome... just not worth an entire idea group), so I usually give this idea group a pass.
Economic - Money is used for a lot of things, and this gets you more of it. A lot more. The development cost reduction also means it saves you monarch points, too.
Expansion - This idea group reeks with mediocrity, it does a little bit of everything, but does not do it very well. If it had a single awesome bonus, it would be a great pick, but the problem is that it is so mediocre that it lacks anything to draw you into it.
Humanist/Religious - You must have one of these. Religious if you plan on purging the heretics and heathens, Humanist if you plan on co-existing. I recommend religious in most cases, unless you have a particular country or religion that is built for co-existing. Rule of thumb is that if you can get heathen tolerance from elsewhere, go Humanist, otherwise, go Religious.
Innovative - Like expansion in that it has a lot of mediocre but helpful bonuses, but unlike expansion, it has a few standout bonuses that make it worth picking. Monthly War Exhaustion, Leaders without Upkeep, and Technology cost. -25% Advisor cost is a lot more useful now that we have level 5 advisors.
Diplomatic - Great for diplomacy-heavy runs. Its main feature over Influence is that it gets +1 diplomat and loses less stab to certain actions like breaking alliance.
Espionage - This is a lot better than I remember it, but it went from terrible to just mediocre, maybe slightly below Expansion in value, without any decent stand-out bonuses.
Exploration - If you are colonizing, you need this, if not, you will give it a pass. I have toyed with the idea of taking this for the sole purpose of questing in the new world for one of those sweet permanent modifiers... but that is a huge investment (800 dip and 1 slot being dead weight for a good chunk of the game) for something that will probably not pay off.
Maritime - If you are a naval power.
Trade - The question you need to ask yourself is, how many trade nodes are you planning to contest? If it is more than 3-5 (especially if you are blobbing hard), then you want this. If not, then you probably will give it a pass, as the main draw from this is the +3 merchants, but those merchants are only good if you use them.
Influence - Similar to Diplomacy, except more heavy on vassals. There is also a 20% AE reduction that is really useful.