The main problem is simply how much space there is for it. A stick with pots is certainly too tall to fit. You can surely wire it in if you use the appropriate resistors, but it would probably not fit in the original throttle handle shell.
The most viable option would probably be a flat sliding style stick like the ones used in the PSP, Vita, and 3DS. I am sure there are specs out there about its voltage and resistance loads. I believe I have read that the PSP stick runs off +3.3V and resistance ranges from 2K to 5K on each axis, and 3.5-4K when centered. The 3DS stick is closer to the 10K range. What were the resistance ranges of the original hardware? The sticks from the PSP1000, PSP2000, PSP3000, Vita, and 3DS all have different resistance ranges. If we're lucky one of the various sticks could match without needing any resistors.
Another candidate is a laptop trackpoint. While it is not as accurate as a stick using pots would be, it would still be a hard upgrade over the current Saitek one if it was from a ThinkPad for example. This would probably take a lot more effort though as usually they are wired as PS/2 devices.