descriptions of each issue:
Missing or worn bushings: Each bus needs one plastic shift bushing in the front, and two in the central shift tube. (Some have three.) It might be possible to shift without the front bushings, but shifting will be loud and inconsistent. Check this first.
Aftermarket parts not compatible with originals: Some aftermarket shifters do not play nice with other stock parts due to height differences, angle issues, and lack of tape measures at the shift rod factory. Some shifters need stock reverse lockout plates, and some do not.
Clutch release issue: Always try all shifter tests with the engine running and with the engine shut off. If your clutch pedal doesn't fully release the clutch disc, the car will shift fine with the engine off but not with the engine running.
Cabin floor damaged: Over-tightening of the shifter housing bolts and front-end collisions can warp the cabin floor into shift issues. This won't cause any issue by itself, but can make existing issues worse.
Loose or missing grub screws: Unless your bus is held together entirely by rust, a missing grub screw will not allow the shifter to communicate with the transaxle shift mechanism. This can show up as hard 2-3/3-2 shifting, and general inconsistency in shifter action.
No grease on bushings: This usually results in loud and firm but still predictable shifting. Metal things need grease to move, like, duh? Rear bushings can squeak and sound like Bowser.
Shift rod(s) bent: So you just removed your front beam but it's hanging up on something Oops Front/back action may be unusable now, and side to side shifter action may be odd too.
Anti-rotation pin missing: This causes the shifter to rotate freely in its housing, but it may theoretically possible to shift, though I doubt it.
Grub screw landing(s) dirty: The shifter grub screws have tapered heads and required a matching taper to grab when tightened. If you get dirt in the landing, or use the wrong bolt, the proper grub screw can not fully tighten. This results in clumsy shifting at best, and a general distaste for going into any gears.
Reverse lockout plate missing or installed wrong: The lockout tabs go up, and the Ramp goes on the Right. See how fun letters are? The "collar" on the shifter handle has to be at the exact height of the lockout plate when the plate is installed into the housing when held upside in your hands. Sometimes the lockout plate will be at the wrong level when aftermarket shifters or plates are mixed with originals.
Nosecone bracket broken/studs stripped: All shifter movement is braced by a thin metal bracket in the transaxle nosecone. Gentle shifting prevents this, but sometimes the bracket or studs can't handle any more force and break. Repair requires removing the engine and transaxle. Remove the 091 springs and circlips while you're in there.
Coupler cage loose: The metal rear shift coupler cage should be a tight fit around the rubber bushings. Slop here results in sloppy shifter feel.
Free space: we've all used this one.
Broken/worn early guide pin or late bushing housing: The front shift bushings on early bays need a straight pin in the front bushing. Bent pins can allow the shifter to pop out of the pipe bowl, and missing pins result in no shifting at all. Late bays have a round hold in a thin sheet of metal that holds the bushing. If the hole is wallowed out enough from neglect, a new bushing will not stay installed. Late model bug bushings seem to work really well in late bays where the quality of available bushings is suspect.
Motor mounts loose/worn/missing: The transaxle has to remain stationary while shifting, like duh?
Bad pilot bearing: The pilot bearing allows the clutch to spin independently from the engine. A bad bearing usually acts fine when the engine is cold and mimics a sticking clutch disc once the engine warms up. Sometimes they make noise. Always they require engine removal to repair.
Reverse lockout plate broken: Reverse lockout plates crack and result in a wandering shifter feel. Originals can be welded, since the cost will out-perform an aftermarket plate. Make sure it matches the shifter housing. ("Wings and cutouts" or "No wings or cutouts.")
Reverse lockout plate misadjusted: Often resulting in a "chirp" of gear grinding when downshifting to second gear, the plate is designed to guide you into second and prevent reverse engagement without a full "push down" of the shifter. The "chirp" is your reverse gear grinding into silver slurry.
EMPI shifter: This was almost a free space, but if you're going to spring-load a shifter, make it the 1-2 gate instead of the 3-4 gate. Those who drive on any public roads need the 3-2 downshift guided if anything at all. Remove the coil spring in the base of your EMPI shifter to retain its excellent Nylon pivot bushings while making it easier to select gears. Adjust by selecting second gear and shoving the whole shifter and housing to the left before finally tightening the shifter bolts.
Coupler collar spinning: Some aftermarket shift couplers aren't fully coupled internally. (Interestingly, NOS VW couplers are crimped 360°, where even the good aftermarket couplers are only crimped once for a few degrees somewhere along the edge.)
Bent shift coupler: Someone removed your engine/transaxle without proper supports and coupler disconnects, so you get to buy a new coupler. And instal it. And adjust the reverse lockout plate. And enjoy paying attention.
Nose cone ball worn/missing: There is a metal ball in the nosecone that is responsible for taking your PERFECT H-pattern (right??) shifting and translate those motions into gear engagements. VW went plastic (cheap!) in 1976 and the metal balls will wear out too if you neglect oil changes and/or shift like a gorilla. Repair requires removal of engine and transmission. Please ensure your old ball is fully removed first, RIGHT KENTps? 
Coupler cage bolts missing: The seemingly-cheap-but-actually-brilliant method of using a lag bolt and sleeve to clamp the rubber bushings into the rear shift coupler can work loose. I make sure to check the tightness on these after the first few hundred miles of shifting. Some use blue thread locker.
Shifter housing bolts loose: This one should be self-explanatory, but those buses are still out there! Mine was one.
Slot/pin interface in pipe bowl worn: The fit of the shift ball pin into the shift rod pipe bowl determines lateral slop in the shifter. New parts are not available, but rotating the pin often results in the "fresh" metal taking up some slack until you find someone to weld the bowl and grind a fresh slot into it.
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I wish everyone many many miles of fantastic shifting,
Robbie
