Being smart doesn't mean you'll always win. I mean, even Shika knew that without much chakra left after the Temari fight he was going to lose the next match (which happened to be Shino). He knows enough about himself to make that decision.

But I'm guessing from the replies you weren't talking about in the tournament but in an all-out battle when both are at their best (since Shika didn't learn his "new move" until after the tournament). Also, to make any fair judgement you have to compare them in the same time frame (i.e. you can compare Shika with his "new technique" with Shino from his match with Kankurou - Shino might have learned a new technique since then as well).

But I would put my money on Shino. I think Shino isn't portrayed so much as smart as he is wise and experienced (and mysterious). Vs Kankurou he showed he had chakra control (hanging on a tree upside-down, which gives you a comparison to Naruto/Sasuke when they were training chakra control in the Zabuza arc), analytical abilities (he noticed Kank was weak in taijutsu), pre-emptive planning (used bug clone at start of fight), and strategic planning (placed bug on Kank's shoulder and use of diversions). So, in fighting prowess, Shino is not significantly inferior to Shika if at all. Shika's IQ makes him a better leader, whereas Shino's prowess and abilities make him a better fighter. Also Shino is probably one of the worst match-ups for Shika, which is someone who has a secondary form of attack outside that of their own body. Look how that 2-headed sound nin was able to foil Shika's plan so easily (when Shika had the 4 sound nins shadow binded).

And I was sort of disappointed at Shino's low character ranking in the latest poll, but what can you expect when we've been given no real info on his past or any appearances in the manga as of late. I only hope his low ranking doesn't affect his chances of appearing more in the manga. I wish they'd do a mini-arc with Kiba, Shino, and Hinata's team as I think it would be cool to see this team as a whole a bit more.

edit: oh yeah, and from comparing Shika's willingness to fight/kill compared to Shino's, it is apparent/implied that Shino would be more willing to take that plunge and kill someone (since Shino had no problems blowing Zaku's arms off).