I would think SpaceX would really just reduce the number of engines, as the current Raptors give sufficient thrust.
Saturn V lifted off the pad at around 2 m/s^2, while the Super Heavy/Starship should lift off at around 3.5 m/s^2 (4400 tons gross, 5993 tons of thrust). Falcon 9 lifts off at around 4 m/s^2. If SpaceX could increase thrust to 250 tons per Raptor, which probably isn't too unrealistic, the Super Heavy/Starship would lift off the pad at closer to 7.5 m/s^2.
You take off more efficiently if you take off faster, but there are diminishing returns here. And reducing the number of engines is also a way of cutting down weight, increasing performance and reducing costs. If they were able to get to 250 tons per engine, and wanted the Super Heavy/Starship to take off at 4 m/s^2, they could remove ~6 Raptors. (And 1-2 Raptors on the Starship.)
Alternatively, they could of course stretch the Super Heavy a bit, like they've done with the Falcon 9. Stretching the Super Heavy by 20 meters would get you down to around 4 m/s^2, and would result in a significantly increased payload capacity. This would reduce the number of trips needed to refuel a Starship in orbit. (The Super Heavy/Starship would then be 138 meters tall, 28 meters more than the Saturn V...)