The Honda factory kits look tacked on because... well, it looks tacked on! For an example of a well-integrated kit, just look at the ground effect accents on the old Protege5, or the current Mazda6's. Now, I know those are not ground effect kits per se, but their chin spoiler, side skirts, and back bumper are all integrated as part of the overall body. Everything is smooth and comes in a 1-piece design.
I like Mazda's approach because the ground effect stuff looks more understated and better integrated. Honda's kit looks more aftermarket (and I dare say, a tad riceier). Different approaches and designs, and they'll cater to different people.
-Rick