If before pressing reforms as absolute monarchy was an extremely hard task, now it's almost impossible. Russia is close to unplayable right now as rebellions became more numerous and now you have to kill EVERY single rebel brigade in each of your 500+ provinces...and as autohunt rebels now go siuciding vs 35k rebel stacks you have to kill all this hundreds of brigades manually.
What are you doing to your pops? O_O
I played Russia like ten times and never ever had any large scale revolt that got out of hand.
Anyway, have you tried increasing your stack size a bit? Once you can comfortly support 30k stacks in your provinces these are more then adequate for rebel hunting.
So far I'm very disappointed with the "one port per state rule". The main reasons are:
1) Ports construction used to be a powerful "Keynesian" tool to drive demand in the early game.
2) The player can no longer be relaxed regarding its navy's size (and therefore costs) because of much less ports to build ships than before. In the old days I could go "the brits have 30 Ironclads more than me? I'll build 40 then!".
2.1) I think the rule preventing me to build large ships outside my Capital's range by land connection is also not a good idea, but I haven't reached far enough into the game to be certain.
3) I think it actually penalises small countries in multiplayer.
(1) The price for ports does significantly increase with higher level. In addition, that early demand was actually partially bad because the game lacks upkeep costs - once these buildings are completed, all the "fake" industry demand is gone and you are left with economicially unfeasible factories once the project is completed.
(2) It does indeed hurt to lose your ships, but late game times from high level ports + techs are not too bad. At the very least it gives an additional incensive to research naval techs - a tree that is often very low priority...
(3) It does indeed. But not to the extend like the naval support limit in EU3 made Netherlands or Sweden almost impossible to compete with other nations before DW came out. However, I guess it might be possible to mod the game and add supply limit to techs to balance out the issue. In addition, the new naval combat system should favor quality over quantity, so tech advantage can be quite important (and SWE has indeed way more RP than ENG).