One game=/=The entire series.
Kamek has been the main antagonist for more games than Baby Bowser.
Heck Baby Bowser was a hero at one point.
Evaluation:
Super Mario World 2: Yoshi's Island/Yoshi's Island: Super Mario Advance 3 has Kamek in lead villain role while Baby Bowser serves as final boss.
Yoshi's Story has Baby Bowser as main villain with Kamek nowhere in sight.
Yoshi Topsy-Turby: Bowser is the main villain. Apparently this game takes place during modern Mario games, as there is no sign of any baby whatsoever. No appearance by Kamek either.
Yoshi Touch & Go: No actual plot to go by. Both Kamek and Baby Bowser make an appearance, however.
Yoshi's Island DS: Bowser is the main villain again, effectively kicking his infantile counterpart away, who then temporarily teams up with the other babies in order to get revenge (i.e. no heroics). Past Kamek makes a small appearace and Future Kamek follows Bowser's orders.
In conclusion:
Main villain roles:
Baby Bowser: 1
Kamek: 1
Bowser: 2
(And this is excluding OTHER Yoshi spin-offs, where Bowser is the main villain as well)
Appearances:
Baby Bowser: 4
Kamek: 3
Bowser: 2
(Again, excluding OTHER Yoshi spin-offs)
So going by this, Bowser is technically the main villain of the Yoshi series (especially when other spin-offs are put into account), and Baby Bowser is the most prominent antagonist. Kamek's in the middle.
EDIT: I might as well explain other spin-offs:
Yoshi: No story, and no appearances by ANY of the characters. Not even Bowser.
Yoshi's Cookie: In the original NES version, there is no story, but Bowser is one of the playable characters in VS. Mode. In the Nintendo Puzzle Collection version, there is a story, and Bowser is the main villain. There IS a Magikoopa that you go up against right before Bowser, but it isn't stated to be Kamek (probably because the character known as "Kamek" didn't debut yet), but for the sake of how people say the character known as "Toad" appeared in the first Super Mario Bros., we'll just count this Magikoopa as Kamek.
Yoshi's Safari: Bowser is main villain. No babies, no Kamek.
Yoshi no Cookie: Kuruppon Oven de Cookie: Have absolutely no idea on this one.
Tetris Attack: Bowser is the main villain, while Kamek is his 2nd-in-command. No babies other than a yellow Baby Yoshi.
So now that means:
Main villain roles:
Baby Bowser: 1
Kamek: 1
Bowser: 5
Appearances:
Baby Bowser: 4
Kamek: 5
Bowser: 5
So throughout the entire Yoshi series, outside of the Yoshi's Cookie sequel as I can't find much information about it, Bowser is through and through the main villain and the most prominent of the villains other than Kamek.
Since we already
have Yoshi's main villain in Smash Bros., we don't really need another one.