There are plenty of intelligent male leads in manga. There are even some intelligent female leads though far rarer. However, I can never find manga where the intelligent ones get together. Smart characters seem forever destined to hook up with a brainless idiot who somehow wins the smart character over with his or her naive "charm." (I seriously cannot take anymore smart!guy x idiot!girl shoujo before I start to hurl.)

The only good example I've read is ES. I'll be so very happy if there are others.

Yuri or het is fine. No BL or yaoi please. Thanks!

Can only think of Kare Kano atm

Special A is another one.

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you can try Zenbu Chodai

I suppose that actually depends on the definition of 'intelligent'. Sure, Kei fits, and Hikari has brains when it comes to school subjects. But, when it comes to some common sense or her own feelings and how to act upon them, she's a dunce extraordinaire.

Cat Street might work. I suppose it depends on how intelligent you find the female lead to be. I think she is, though she is socially awkward - which shouldn't be confused with being an idiot or dense.

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If you've ever thought or said "Nice Guys finish last" and really meant it, then you should probably read this LJ post by DivaLion. It's incredibly insightful whether you're male or female.

From a bumper sticker I like:
"If you're gonna ride my ass, at least pull my hair."

At the moment, I have my eye on Promise. The scans are only two chapters in, so it's hard to tell if it will turn out smartxsmart.

MAX Lovely!

And uhh, Kare Kano would fit too.

It's so hard to find a good romance manga without a ditzy girl lead or a loser guy lead.

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The sweeter the apple, the higher the branch. The quieter the fart, the nastier the smell.
GUESS WHO??

hmz not sure if this is what your after but these are what I would term as 'intelligent' in the sense that the females aren't stupid and have a backbone although at times may be naive to some things...

[m]Kaichou wa Maid-sama[/m]
The One
Kare wa Tomodachi
Papillon - Hana to Chou
Ingenuo

Akahime Ranshin - Literature professor falls for her student who is a gifted kabuki actor.

Akagami no Shirayukihime - Really smart heroine and an intelligent prince.

Basara - They're both pretty damn intelligent and mature as well.

Any romantic story by Midorikawa Yuki. None of her characters are dumb, seriously.

Blue Ramun - Doctor falls for military commander. Both are intelligent.

Tokage Ouji - She's a smart, thoughtful girl; he's a quiet, geeky lizard-prince.

Yet to get together...

Glass Mask - they haven't "gotten together" finally yet, but she's smart and no matter who she ends up with, it'll be an intelligent romance. It's pretty obvious who she's going to end up with, anyway.

Ashita no Ousama - same as above, the manga hasn't ended yet but the intelligent girl has her heart set on someone, and there are other intelligent male suitors. (KAZUMA RIN! <3333)