"Wouldn't have it any other way" means that even though an experience was difficult, you wouldn't change it because you learned a lot from it or it made you a better person. It's usually used to describe something that was a struggle, like taking care of a sick parent, being a soldier on a battlefield, or having a hard life. I think the phrase is a bit too dramatic to describe the task of learning English. In your examples, #3 is the most clear. However, if you're trying to say that you don't mind the hard work that it takes to learn English, you could reword it. You could also replace "I wouldn't have it any other way" with a different phrase: Learning English requires a lot of hard work, but I don't mind. Learning English is a difficult task, but it's worth the hard effort. It takes a lot of studying and hard work to become fluent in English, but it's worth it.

1. It's never easy having spoken English fluency but I wouldn't have it any other way. This sentence is correct grammatically, but the meaning is strange. It says “when you are fluent in English, it is not easy.” It must be very difficult for all English native speakers, like me! Better: “It’s never easy to obtain fluency in spoken English, but I wouldn’t have it any other way.” 2. It's never easy having command of English but I wouldn't have it any other way. Better: “It’s never easy to reach a level where you have good command of English, but I wouldn’t have it any other way.” 3. It's never easy becoming fluent in English but I wouldn't have it any other way. This is fine. You could also say “It’s never easy to become fluent....” Also, “I wouldn’t have it any other way” means “I am happy that it is not easy- I prefer it to be difficult.” I hope that’s helpful!