は and が and the differences between them, especially in practical usage, are notoriously difficult to explain. Remember that this is just my own personal interpretation. I am sure there are other and perhaps better "textbook" explanations. When I was learning Japanese I tried to think of shortcuts, too (kind of like a "duct tape" solution: it doesn't really fix the problem, but it gets you through temporarily until something better comes along!), so I wouldn't have to worry so much about the finer points of grammar. Therefore, let me say that I hope in this attempt to help you, I do not confuse you any further.
My first bit of advice is to brush up on whatever your textbook says the differences are between the two. With that info in mind, let's continue.
OK, so let's make the sentence consist of nothing but
空がきれいで気持ちがいい
I think as the sentence is written above is the best way to write this sentence.
Next, think about changing the first が into a は.
空はきれいで気持ちがいい
How do you think this changes the meaning of the sentence?
You can either think of the subject changing from an understood "I" to the sky, OR, there's a slight shift in nuance so that it almost sounds as if everything else is dirty(!). But neither of these things, do you want to say, do you? (When did Yoda enter my body?!?)
OK, so let's keep that が intact, and instead change the second one. Our new sentence is:
空がきれいで気持ちはいい。
Here, for reasons beyond my ability to explain, the subject will stay at the understood "I", so that changing of subject issue is not a problem.
But again, it almost sounds like there's SOMEthing amiss. Like, kimochi is good, but nothing else necessarily is. It's hard to explain. But maybe there's a situation like this: the subject of this sentence, "I", has a problem that has been going on for some time. S/he is very worried or troubled by this problem. It is one of those feelings that just won't go away until the problem is solved, but there's no end in sight. So today, "I" walks outside and lo and behold, it's a beautiful clear sky. S/he feels good, BUT there's still that nagging feeling that remains underneath.
Another way to think of this, in reverse order, is as follows:
気持ちがいい
is for the most part a set phrase. It's just the regular standard way to say it.
空がきれいで
is a subclause in the main sentence. Therefore unless you want to specifically single out 空 as something in contrast to something else, the default is が. This is one of those "shortcuts" I was talking about earlier.
I hope this helps! (I REALLY hope this wasn't confusing. I offer my sincerest apologies if it was.)
