The GameCube control pad just wasn't built for 2D beat 'em ups. Take a look at the directional pad - it was built to be treated like a second set of individual buttons, pretty much the way it been treated so far. Then there are the four main face buttons, which are clustered for simple control systems, not attacks and blocks arranged by force and limb. And despite the developer's best efforts to the contrary, Capcom Vs. SNK 2 EO never really feels right.
That said, there is one significant thing which cannot be blamed on the hardware, and that's the state of the port. Changes to the make-up bring it more into line with the Cube control system, but graphically it's unchanged from the PS2 and Dreamcast versions, which were released nearly a year ago. That's not to say the graphics are bad, but however smoothly they are animated, Capcom's 2D designs are ageing quite quickly, and the opportunity to revamp them for this Cube version has been overlooked.
The biggest change to the Cube version of the game is the concept of -isms. AC-ism is the old-school approach, which most people will stick with, allowing you to fight your opponents and execute special moves in much the same way as always, but those of you without any experience in Capcom fighters may find the GC-ism a superior approach, and a good way of getting into the series. By mapping various special moves to the C-stick, Capcom removes a lot of the challenge, but also allows you to get the hang of combining them to gratuitous effect. That said, the idea is that you can progress to the AC-ism after a while, and this would be tricky with a Dual Shock II, but the Cube's directional pad really doesn't help.
There is also a question mark hanging over the structure of the game as a whole, even aside from port issues. For a start, the choice of characters is at best unadventurous, and at worst somewhat lazy. The box boasts "over 44 characters" from various Capcom and SNK fighters, but when you consider how similar Sakura, Akuma, Ryu and Ken are to one another, and that this isn't the only example of closely related characters - both in terms of gameplay and graphical design - then the number seems slightly less impressive. That said, you can pick between six "grooves" for the various characters, which alter the way you build up super moves and other aspects of your battle strategy. Pitting Ryu against Ryu, even if you reckon you and your mate are as evenly matched as can be, can still produce varied bouts if you opt for different grooves.
Capcom Vs. SNK 2 EO is a brave attempt to port an excellent 2D beat 'em up to a platform which doesn't really want to play ball, but various problems on both sides conspire to thwart the effort. The GC/AC-ism system is a nice idea, but it oversimplifies and suffers at the hands of the Cube's dodgy dpad, and the game itself is growing older with every passing day. If you want a 2D beat 'em up for your Cube, this is definitely your best choice, but it might be worth investing in an arcade stick or a third party pad if you want to get the most out of it.