The gemara (Sota 34) darshens that the names of the meraglim reveal their flawed character:
תניא, א״ר יצחק, דבר זה מסורת בידינו מאבותינו, מרגלים על שם מעשיהם נקראו, ואנו לא עלתה בידינו אלא אחד, סתור בן מיכאל, סתור – שסתר מעשיו של הקב״ה, מיכאל – שעשה עצמו מך א״ר יוחנן, אף אנו נאמר, נחבי בן ופסי (פ׳ י״ד) נחבי – שהחביא דבריו של הקב״ה, ופסי – שפסע על מדותיו של הקב״ה
It seems that these were not very nice guys. However, Rashi tells us
כלם אנשים – כל אנשים לשון חשיבות הוא, ואותה שעה כשירין היו.
Indeed, if the meraglim were as bad as their names suggested, it begs the question of why Moshe selected them for the mission. Why invite trouble by choosing the bad apples?
Furthermore, why would Moshe have davened only for Yehoshua if he knew that the other mergalim were going to cause mischief? Aderaba, he should have davened for them, as they were more in need for his tefilos than Yehoshua!
Transitions are difficult. Ibn Ezra famously writes that even though Bn"Y at Yam Suf vastly outnumbered the mere 600 chariots Pharaoh had, they would not have been able to fight. Psychologically, they could not stand up to the people who had been their masters just a short time earlier. The transition from slavery to freedom is not so simple. Bn"Y in the midbar were surrounded by the miracles of the mon, the be'er, the ananei ha'kavod. All their needs were miraculously taken care of. The transition to life in Eretz Yisrael, a life of working the land, a life that would require their effort, not miracles, to create a all the trappings of a functioning country, was bound to be difficult as well.
The gemara does not mean that the spies were at that moment flawed individuals. What the gemara means is that the 12 spies were flawed individuals who had managed to overcome the defects inherent in who they were and become better people. Each one of them, as their name indicates, had a weakness. Each one of them managed to make the transition to greatness.
Who better, writes the Tiferes Shmuel (Aleksander), to lead when facing a period of national transition? Who better to see and explain how a wasteland inhabited by immoral, antagonistic enemies can become gan Hashem?
This is why Moshe prayed for Yehoshua alone. It was davka Yehoshua's great piety which gave rise to Moshe's concern that he, more than the others, would not be successful. Not having to overcome any inherent flaw, not having to make a transition to become something better than who he was "meant" to be, was in this case, in Moshe's view, a defect.