Well, all agent gains in EU3 are independent from country size, so you can´t fault Paradox from being consistent. Also, while larger empires have more manpower, it also requires a larger bureaucracy to run. Finally, as mgistrates IMO represents governmental influence, you could argue that a smaller nation´s central government has an easier time meddling in local affairs than a global empire.
Exactly. Only valid criticism here is the lack of naval tradition. This is due to the fact that naval wars are often decided by a single battle, so the tradition gained is negligible.