Part of the fun of this game is that there are many different ways to win. If someone wants to do a deadball strategy, and they can make that work, good for them! If someone wants to try a fatigue strategy, go for it! Whatever a player thinks will help them get the win, I say they should give it a try--with the exception of collusion, and I've rarely seen anything that makes me even suspect that.
Over the history of this game, it has been updated to eliminate certain loopholes and make it closer to real baseball. Maybe (though I'm not holding my breath) this new management will find ways to improve the game to bring it even closer to a real baseball sim. Even then, there will always be some level of non-realistic strategies being used, since we all know baseball is much more than the numbers game it is on WIS.
To me, when I see a strategy being used that irritates me, I use that as more motivation to try to find a way to beat that strategy. Is everyone nerfing your power hitters with deadball pitchers? Spend your money on OBP and fast runners. Is everyone using high OBP and steals? Overload your team with low walk pitchers and A+ catchers. How do you do that against those who "abuse" the fatigue system? Figuring that out is one of the fun and challenging parts of the game. In the end, I think the best overall strategy is to make your team better than anyone else's so you don't have to worry about whether they throw a few games here and there!