I have been running a campaign for the last 2 years and there have been multiple NPCs tagging along with the party at various times. But none that I considered my PCs. They were little more than an afterthought. They had their support role, and if the party wanted them to stay, they stayed, if not, they left. There has been one NPC Cleric who has been with the party from the beginning. He is very non-descript and typical of any NPC cleric of his level. I could probably take the example NPC out of the DMG for his level and this particular Cleric in my campaign would be so similar it would be eerie.
The party members have always insisted he stay. I admit that I have found myself bothered by continually having to monitor him throughout the campaign. But after 2 years and 13 levels, the party is loyal to him and vice versa. I do find that whenever the party is lost and at a crossroads in the plot, a couple of players try their best to find out what the Cleric thinks they should do, as if maybe I will slip up and use the Cleric as a plot device or try to steer them in the right direction. 99% of the time he shrugs noncommitally and asks them what they think.
He died twice and both times the PCs did not hesitate to have him raised and brought back into the group. (I even attempted to suicide him once about a year ago when I believed it was necessary to aid me in speeding up my game management. I vowed never to do it again, unless it was for good roleplaying reasons, not for metagame reasons.)
The bottom line IMO is that it is ultimately about the players. The GMs role should be that of referee or mediator and to keep the game going. Everyone should have a good time, as it is a game. The Gm already has the attention and spotlight in normal circumstances, and should not seek to steal the glory and thunder from the players. If the GM is spending his best efforts on a PC he controls in his own game, the game is probably suffering in many other areas from his lack of focus.