True, on the surface, Yahoo has a good solution. However, they do not allow for much flexibility and the system can be difficult to work with if you have a complicated product line with lots of sizes, colors, options, etc. We tried like crazy to make it work, but had to abandon Yahoo for other solutions that allowed us more control (Perl, MySQL, etc.) Again, if your product line is kept simple, Yahoo solves lots of expensive problems with a minimum of hassle. My 2 cents.
—Brad "Don't ever take a fence down until you know the reason it was put up. " G. K. Chesterton
True it can be difficult in some aspects (though you can get around almost everything with enough know-how and effort) but there are a couple of counter points. You could just link to the cart and host it elsewhere and also, they have a new system (StoreTags) that is just tagged based so you can design your site with any tool you want.