Owned both more than once and my verdict is Shadow all day long in every department. From layout to rules to sound to music to art.
Congo is ok but it has the DUMBEST gimmick playfield in pinball history, the stupid monkey game that is impossible not to beat, and way too many dumb video modes. Every game seems the same to me, always follows the same "path" with the same awards in the same order and such, and way too much "stop and enjoy this video mode/monkey game" stuff. I get burnt out on it pretty quick.
The battlefield > monkey game
One fun video mode > 5 dumb ones
Sick silver Pistol > plunger with endless repeatable skill shot
Layout = both pretty good but I favor Shadow
Rules/ sound / music - I personally favor Shadow but like everything that's subjective.
Congo I liked at $900 12 years ago but at current prices I really think they are overrated and overpriced. I'd have no problem paying current Shadow prices if I were in the hunt, it's a better game.