Again, this isn't difficulty. When you handicap the player you incentivize them to go after what is meta and/or ways of bypassing the handicap. Handicap, or AI buffs, encourage the players to meta game the game.
In your example if ideas were 50% more expensive what a good player should do is go after a select few idea groups over, and over, and over again because the cost-benefit isn't really there. You would also see a lot of idea groups never be finished for the simple fact that you'd need to conserve your resources for other stuff. Similarly getting -1 MP in each category would make it so that players would spend less on what isn't optimal and same the points for what they really need.
See how you aren't Incentivizing new strategies but rather decreasing the number of possibilities that a player have at their dispose? This isn't increasing difficulty, no, it is forcing optimal play on the player.
A series that suffers a lot more than EU 4 in this is Total War where there are so many game rules that buff the AI and handicap the player on higher difficulties (AI getting buffs for melee combat on their units, player's armies getting disproportionately more expensive the more troops you have) which all converge into making the majority of all factions roosters useless, push all armies to be composed of the exact same types of units, and forces players to only play what is optimally (unless the player is exceptionally competent).