I think that they're ultimately differences in the prefactors (or at any rate, lower-order terms), much like the differences between different possible architectures for classical computers (integrated circuits, vacuum tubes...). Fault-tolerance should ultimately "work" in all of them, and yield the same class of problems solvable in quantum polynomial time; it's mostly a difference of how expensive and hard are the engineering problems are. The biggest difference of this kind is that superconducting qubits are fixed in place on a 2D grid, whereas with trapped-ion and neutral atom qubits you can pick them up and move them around. That's a huge advantage for the latter, maybe more than compensating for their 1000x slower gate speed. Even there, though, we're talking about lower-order factors, since even with superconducting qubits, you can simulate all-to-all connectivity more slowly by using cascades of nearest-neighbor swaps.
I think that they're ultimately differences in the prefactors (or at any rate, lower-order terms), much like the differences between different possible architectures for classical computers (integrated circuits, vacuum tubes...). Fault-tolerance should ultimately "work" in all of them, and yield the same class of problems solvable in quantum polynomial time; it's mostly a difference of how expensive and hard are the engineering problems are. The biggest difference of this kind is that superconducting qubits are fixed in place on a 2D grid, whereas with trapped-ion and neutral atom qubits you can pick them up and move them around. That's a huge advantage for the latter, maybe more than compensating for their 1000x slower gate speed. Even there, though, we're talking about lower-order factors, since even with superconducting qubits, you can simulate all-to-all connectivity more slowly by using cascades of nearest-neighbor swaps.