I don't know if this'll justify a 500 Wii point purchase for you, but the Wiiv ersion really feels like the more natural way to play the game.
So, yes, you have vastly improved visual stylings. The stick figures in the Flash game are functional, but there's something wonderful about tongue depressors and bottle caps. This is not a question about graphical prowess, but rather one of aesthetic pleasure, and the WiiWare version is so much more unique and prettier to look at.
And yes, 4-player is a pretty significant addition. I wish every game had co-op. *sigh*
But in addition to that, the Wiimote just feels a whole lot quicker and more natural than the mouse to me. Both versions will give you carpal tunnel I guess, but I have to say that the Wiimote felt a whole lot less stressful to use. And you've got a full-screen game with more real estate, but it's actually easier, in my opinion, to grab guys in the Wii version.
Additionally, the Wii version makes several friendlier design decisions. You don't have to worry about upkeep for one, and in a level they track your level score, so the number of points you actually earn at the end is much more transparent instead of the convoluted way the flash game tabulates it.
Additionally, you don't seem to be able to "throw" the enemies into the temple in the flash version, whereas in the Wii version you can learn how to "toss" your enemies in an arc such that they land in a ready-to-accept them pit of conversion. It's small things like this that really streamline the experience of simple games and make the difference between a response of "it's a neat concept" and "I can't stop playing this oddly polished experience."
Yeah... you know, I NEVER tried the internet flash version until now, and now that I have, I totally feel fine with my $5 purchase. The flash version has the basic gameplay, but it lacks the polish, spirit, and smoothness of the WiiWare game. These are subtle differences (except the ease of use of the wiimote, which is a MAJOR PLUS), but they're the sort of differences that make me much more receptive to the experience versus the internet flash game.
Plus I can play this game from bed.