This is starting to really bother me - the acceleration is so poor I often find myself downshifting to third gear to squeeze some extra power.

Configuring the throttle body does the trick, you can really tell the difference while flooring it. A day or two later the engine is back to it's miserable state.

 

Driving a 1.4 MPI feels a lot better, almost instant throttle response, the engine picks up revs more easily, in comparison the 16V feels like you're trying to force a dying horse to move.

 

Also about the throttle response, is there anything that might improve it? Feels like there's a two second delay, really noticeable when starting from a full stop.

 

I'm well aware the engine cuts power if you use RON 95, but for the last year or so I'm using RON 100.

 

The only way this car could ever produce 100 HP is if it was falling off a cliff

 

The throttle body is clean, I'm really hoping that this isn't the best the engine can do. If it is, I'm really disappointed.

It does sound like there is a fault with the throttle body since re-adapting it cures the problem. I suggest you start by fitting a good second-hand throttle body from ebay or a scrapyard, they're not very expensive, the same part was used for many different VAG models. Also have a look at the wiring loom since it is often very tight at the throttle body and there may be some damage to the sense wire.

Nothing to add to the above technical advice but some encouragement. I've had a 1.4 MPI and a 16v and they are like chalk and cheese. The MPI was agricultural. The 16v quite refined and much quicker. So hopefully sort the problem. You will enjoy the 16v when it's fixed!