Too early to tell who is going to be better. But this upcoming season can give some answers. Spezza will play on the 1st line in NHL for the contender, Malkin on the 2nd line in RSL also for the contending team. Also Malkin will have a good chance to go to the Olympics (even though there is some abundance of centers: Fedorov, Zhamnov, Datsyuk, Yashin, Kozlov and Malkin, but I guess some of them will be sent to the wing).
I've seen Spezza only once, in juniors, and he looked good, especially in understanding of the game and playmaking, his wristshot seems very good too. But also he looked heavy, I mean Kovalchuk-like heavy (though he is listed only 206lbs) and no legs of Kovalchuk. But I heard that he has improved his speed greatly, so will see.
Malkin's best quality is also very good understanding of the game, other than that: very soft hands with long reach, fast effortless skating, good physical game. Don't forget that Malkin more than 3 years younger (just turned 19) and still developing. He doesn't look as a complete player yet, I mean it is still notable that he has resources to work with and he already looks very good. He is almost 6'4 but looks very fast on his skates, skates without effort (his skating is not as good as Fedorov or Zherdev but speed-wise it is very good). Partly it is because he is not very heavy (about 192lbs) but at the same time he is very strong physically, doesn't avoid rough stuff. I think in the future he has a chance to be close to Fedorov's 2-way game and statistical-wise a PPG player or more.
At international level (mainly, I take juniors) I think Malkin is surpassing Spezza.
PS: yesterday Malkin scored on PP and Metallurg beat Salavat 1-0 on Romazan Cup. Today Metallurg plays vs AK-Bars.