As far as the shooting gimmick in the center, they are extremely similar (Steve Ritchie admits to it). As far as layout goes, you can argue they are a bit different. Spider-Man has lots of ramps, while AFM has more orbits than anything comparitively. AFM as a result, from what I have seen on location, is casuals tend to gravitate toward it more (brilliant Brian Eddy design; "easy to learn, but hard to master").
I'd go ahead and grab the Spider-Man and WH2O. I agree with Robin, in that you can easily sell/trade the Spider-Man later if you find an Attack from Mars. People are always looking for Spider-Man, as it does very well on-route, and is very popular with collectors too. White Water you'll love. I got one, and I wouldn't get rid of it for the world. Super fun game to play, and it still doesn't get boring. Dennis Nordman really out-did himself with the game design.
As far as pinball clones/copies go (excluding the obvious ones in the EM era), I'd have to agree that Medieval Madness & Attack from Mars are the closest you'll get to a cloned pair; barring the inclusion of a game-defining toy.