I thought the flexibility of changing controls was great for a 3d game this old. I switched to WASD, put sniper on right mouse and zoom-in on middle mouse and it was fine. I had turbo on both toggle and hold-shift, but I usually used toggle as turbo felt better unless there was some precision platforming to do.
Well, except for the falling and end-of-level tunnel sequences where the key controls would break as you note.
My big annoyance with mortar and things like it is that the sniper rifle would default to whatever special ammo I picked up (usually not what I wanted), and it was hard to know what other ammo types I had. Cycling through them was slow, and I usually didn’t want to stay in sniper mode for long.
