By the time Napoleon was fighting the Prussians, he'd already created what would in effect be deemed a modern war machine and one that was capable of being steered by Napoleon in central command.

Napoleon's war philosophy as discussed in "The Campaigns of Napoleon" by David Chandler lists these core principles for a campaign:

1. An army must have a single line of operations
2. The main army should always be the objective
3. The army should move so as to be able to place itself on the rear or flank of the enemy
4. the army should turn the most exposed flank
5. the army's lines of communication must stay safe and open.

To achieve these outcomes Napoleon employed three core maneuvers:

the advance of envelopment

central position

strategical penetration

Napoleon's Grand Army was a fully formed thing following the Campaign of 1805. Napoleon had full control over the French War Effort, and remained the inviolate commander for all battlefield decisions. The 1805 Campaign also saw him perfect his use of the cavalry corp. The role of the cavalry cannot be overstated: not only were they used with support from their famous "square formations" but would provide feints, be used to turn flanks, shield their own flanks and serve as a screen to disguise the French Army's movements.

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In this sense we should consider that Napoleon's battles and campaigns to this point had refined modern warfare as Europe knew it.

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On the other hand, Napoleon feared the Prusssian Army's reputation, but it's main fear to that point was based on historical prowess. In reality, the Prussian army has 171,000 effective soldiers in August 1806, and most of their war strategy was essentially from Frederick the Great. Their Chief Command was 71yo, Blucher, their ablest on the battlefield was 64. The Prussian army lacked a staff corp, and it was well known that their plans of campaign had little relevance to Napoleonic warfare.

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To give an idea of how quickly Napoleon could adapt to a threatening situation, while Prussia was mobilising, to gain an advantage, Napoleon formed most of the campaign across two days in 102 orders known as the "General Dispositions for the Assembly of the Grand Army".

Without going into the battles themselves, you could argue that the Prussians lacked modern warfare plans; the Prussians lacked a clear central command and war policy against Napoleon who had complete and unwavering control of his army and its movements. He possessed great ingenuity and used it to take calculated risks against some unknown variables - research batallion carre' which worked well against the Prussians.

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