I've seen cars with bad bushings on the ends of the shift cables have stiff shifting problems. The bushings in the rubber grommets seize on the shift tower levers. Vehicles with a u-joint style shift linkage like a Honda has can also be hard to shift when the u-joint rusts up. Not sure which type you have but they both types are ones you can look at yourself. The rubber grommet type can be made to work better by lubing the rubber grommets in the "eye" end of the shift cable if the bushings are rusted to the shift tower levers. Works pretty good if not replacing the cables. Might need a wider diameter washer to hold the cable end to the shift tower lever. The u-joint type can be soaked with PB Blaster or other good penetrating oil and then lubed with a spray grease so it soaks in and sets up.

Have a transmission shop inspect and adjust the linkage. The linkage is what connects the shifter rod/stick to the tranny.

Good Luck!

Stop searching for a problem that is not there. If it shifts great while moving it is doing what it is suppose to do.

Check your clutch... That can also cause this problem

I just recently got a 2006 pontiac g6 gtp 6 speed manual and over time the shifter has become unsmooth. I can be sitting in a parking lot shifting through the gears (yes the clutch is fully depressed) and it feels as if there is tons of dirt stuck in the track for the shifter. Shifting in 5 and 6 gear is smooth but 1,2,3, and 4 aren't smooth. There is no difference when i am moving. If you can offer an explanation for this that would be great, Thanks!