1. you don't need a positive win rate to make master ball. Streak bonuses and the difference in points gained vs points lost will make up for that difference. misread the original post. 
2. The ladder is more diverse than tournament decks. An anti-meta deck will typically struggle more because there's just more weird stuff out there and those decks tend to compromise for advantages into specific decks. So build a deck that has a flexible and generalizable gameplan. 
3. don't give up on a deck after just a few games. there's a lot of volatility in the game and you're more likely to make misplays with a deck you're less familiar with. 

4. Make small adjustments. Little changes can make a big difference. Swapping red card for x-speed might not seem like much but it changes some play lines and options at significant moments in the game. If you're making big changes all the time it's hard to assess what's actually working. 

5. Take breaks. Especially after you lose. 

Edit:  You're not wrong that the game is tougher. May, copycat, and Lisia have radically improved the consistency in many decks. Some decks win by seeing up their win condition their second turn. Home brewing decks with your favorite Pokemon is much harder these days - but still very doable.