The arguments about weight to orbit are moot. The only thing worth looking at is price.
If the payload is lighter, it still needs to get to orbit, but recovering the stage will eventually make flights cheaper.
If the payload is heavy, the stage simply won't be recovered.
F9 flights to GEO won't used recoverable stages, at least for now.
Yes, the solution is simple. I'll give example figures here.
If the minimum that the engine can be throttled down is 50%, then you don't throttle it to 50%, you throttle it to 60% and start breaking LATER than you would at 50%.
If you're slowing down too quickly, you reduce the thrust. If you're slowing down too little, you increase thrust.
No need for any ascent performance loss or engine re-engineering. No need to hover either. Just wastes fuel. The only thing that matters is the velocity and orientation of the rocket at contact. If you get there by hovering down to it at 0.1 m/s or wildly slowing down from high speed, it makes no difference.