If gas mileage is no problem for you, definitely 3.5. If prices for both are similar, that's more value for money.
And then again, if your route does not allow you to open up the throttle and enjoy the benefits of a V6 engine, you might as well get the 2.4, which would be just as comfortable and enjoy the improved gas mileage instead. From my experience with the 7th gen Accord 2.4 and 3.0, in typical, mundane, low speed Metro Manila city driving, there is hardly any difference in the way it drives at all.