Oh, no not at all! I was attempting to imply that the Russians aren't pretty little daisies just waiting to be stepped on. Both the PLC and Swedes had the potential to spell the end of Russia in some alternate universe-- the fact that they didn't is fairly impressive. Be that as it may, during this time period Russia wasn't quite on equal footing or better footing than say the Ottomans until nearly the end of the game. So western expansion (or southern expansion) should be somewhat of a challenge for a player.
Russia has much worse starting base tax compared to PLC or the Ottoman Empire so this relative starting weakness is somewhat modeled into the game.
"Be that as it may, during this time period Russia wasn't quite on equal footing or better footing"
That depends on how you define "equal footing" and "the end of the game". If you define it by 1650 (Kmelnitskiy uprising; PLC was never the same again after that) it is fine by me. Which should be followed by the Northern War (1700-1725; Swedish Empire was defeated into second tier European power by Russia). It was the very same Swedish Emprie which occupied the half of HRE during TYW so it was a force to be reckoned with.
The game is loosely based on history. Times of Troubles is incorporated into the game while Khmelnytskiy uprising is not (while it could easily be; rebels wanting to defect to Russia with total forces equal to PLC's forcelimit). PLC most of the time survives and thrives with no rebels/ government problems which is very far from any sort of historical truth.
"In the 16th century, no single person or small group dared to hold up proceedings, but, from the second half of the 17th century, the liberum veto was used to virtually paralyze the Sejm, and brought the Commonwealth to the brink of collapse." "In the period of 1573–1763, about 150 sejms where held, out of which about a third failed to pass any legislation, mostly due to liberum veto. The expression Polish parliament in many European languages originated from this apparent paralysis."
Does this mean PLC needs 50% LA in their provinces in the second half of the game? Probably so.
Times of troubles was quite bad (but that's the only time period when "the fact that they didn't is fairly impressive)" but most of the PLC's post 1650 history was quite bad too. On a side note Austrians could not defeat Ottomans on their own (siege of Wien anyone?) while they can do that in the game. Austrians can also miraculously hold off French while IRL, you know... Grayskin was not possible IRL and yet it forms almost every game in 1.8 without player intervention when Catholics win the war (or if it doesn't start at all which also happens often). That's all (except for Grayskin) has gameplay design reasons rather than historical accuracy considerations.
EU4 is a fantasy game. Its main problem is that the balance of powers does not change between different time periods. Corresponding events (such as national decline for Sweden) are mostly very weak in terms of their impact and unit pips differences between broad tech groups do poor job as well (except Ottoman decline probably). The nations are balanced around some average strength for the time period (and it tends to weigh 1825 more heavily for obvious reasons) so there is little value in comparing Russia's state in 1598-1613 to its "intrinsic" strength. It's a very brief period on time in the context of 1444-1825 scale. In that terms PLC is much more of a total miss for PDX because PLC ceased to exist and there were rather small chances to avoid this.
1 Russo-Turkish War (1568–70) Ottoman military defeat
2 Russo-Turkish War (1676–81) Ottoman victory
3 Russo-Turkish War (1686–1700) Russian victory
4 Russo-Turkish War (1710–11) Ottoman victory
5 Austro-Russian–Turkish War (1735–39) Concession favoring Russians and Austrians
6 Russo-Turkish War (1768–74) Russian victory
7 Russo-Turkish War (1787–92) Russian victory
8 Russo-Turkish War (1806–12) Russian victory
9 Russo-Turkish War (1828–29) Russian victory
That said balance is mostly fine (for a human). AI is quite bad but not only for Muscovy but also for France and Ottomans. But that's yesterday news. Any skilled player can defeat France with Theodoro or occupy Russia which was absolutely impossible IRL (past times of troubles). AI blobs were much more exciting to compete with in 1.7.