If the clutch disk wobbles, it won't release cleanly and initially getting to gear from a stop is harder. Later, changing gears is harder too. Either the hub is going out on the disk, or the pilot bearing is gone. Holding the pedal down at stoplights kills the pilot bearing. A less likely possibility is that the pressure plate is bad and won't release properly.
Yes the trans could be bad too, less likely, but you better take care of everyting before the 3 yr/36,000 mile warranty is up. You are on your own on the clutch over 12K miles (and the stocker isn't worth putting back in anyway, imho), but the trans would be very expensive on your own after 36K.