I agree with your main point, btw.
However, both on paper and from real-world experience, I dare to say that the judicative is the least troubled arm.
In most of Europe, the legislative and executive are pretty much identical and that bothers me to no end. Parliament passes laws and parliament elects the executive, and all the executives (ministers, etc.) are also members of parliament. These two arms are not seperated at all. The USA has the better system there, even though it is still imperfect in that the same parties exist in both.
If I were to re-write the political rules, I'd seperate the arms completely and make a law that political parties can be active in either the executive or the legistlative election processes, but not in both and any attempt to do so leads to immediate dissolution of the party in question with all assets seized and distributed to the poor.