Sakurai stated awhile ago that he doesn't want to create too much emphasis on Japan-only characters, and he's already added a playable character from Earthbound only seen in Japan, and an assist trophy that is Japan-only as well. I think it's a stretch in their eyes to add another Japan-only character. A lot of people have no idea who Lip is (sadly.)
Not that this really matters much, but there aren't any Japan only ATs yet. If you mean Devil, his game was released in Europe.
Even if Lip herself isn't known around the world, her series definitely is. Panel de Pon/Puzzle League rivals Dr. Mario in terms of Nintendo's best selling puzzle franchise (well, those are basically the only 2, but they're still popular). Among Japan-only characters, Lip is certainly one of the more prominent ones. Look at the official Panel de Pon website (
http://www.intsys.co.jp/game/panepon/). It updated for 10 years, receiving tons of fan art and other things. Even the comments section still has a good amount of activity. Sakurai also stated that adding only popular characters doesn't excite him anyway.
And I know that Samus' screw attack is an item and Samus can also perform it on her own, but this is completely different than Lip's sake. Samus can perform the screw attack without the help of the item, as she knows the move, but with Lip's stick, Lip actually uses the item in itself, how could she use the item and use her very own Lip's stick as a move at the same time? It just doesn't work in my mind. If Lip is a playable fighter, she NEEDS her wand, as that puzzle game doesn't offer her much for a moveset.
Actually, Samus needs to gain the screw attack item before she can perform the move.
Not to sound rude, are you sure you actually played Panel de Pon? The Lip's stick doesn't actually do anything. It's for storyline purposes only. In the game's story, it protected her from the magic rain that brainwashed her friends. However...
SPOILERS
If you beat the game on Super Hard without continues, you find out the whole thing was staged by Lip's mother to test her abilities, which essentially made her stick pointless.
The whole making people sprout flowers from their heads thing was invented solely for Smash Bros. As far as a moveset is concerned, she could do plenty, even without the Lip's stick. For her specials, she could use her Watabou as a recovery move, drop garbage blocks, and shoot out flowers. I don't think giving her her wand would be much of an issue anyway. It's not like it's some kind of one-of-a-kind item. We can presume that even in the world of Popples, more of these wands exist. If she had it, she would probably only use it for a few of her attacks (as in, when she actually hits people with it). Maybe only her smash attacks would cause the flowers to sprout.
As for Lip's popularity, she has her fair share of support. In the poll from way, way back when Sakurai asked fans which characters they'd like to see in Smash Bros. 2, Lip got second place in the "Other Famicom/Super Famicom characters" category, losing to Sukapon. She beat out Pit and Ice Climbers, who did make it.
(
http://www.nintendo.co.jp/n01/n64/software/nus_p_nalj/smash/PostResult3.html)
As well, in the questionnaire, a fan tells Sakurai they'd like to see more female characters like Lip in Smash. Sakurai responds that he personally thinks Panel de Pon is a masterpiece, but conversely, he hypothetically asks how well known she is. It at least shows Sakurai has a soft spot for Panel de Pon.
(
http://www.nintendo.co.jp/n01/n64/software/nus_p_nalj/smash/PostReturn009.html)
And of course, more recently, Lip was mentioned in Sakurai's suggestion compilation twice. I know that it doesn't seem to mean that much, and many characters were mentioned more than once. However, the people who suggested Lip ONLY suggested Lip (well, in the second case, it was Lip and Furil) and gave extensive reasons why she should be in. Apparently it grabbed Sakurai's attention. Most of the characters who got multiple mentions were part of longer lists of someone suggesting multiple characters.
Another thing to ponder is the fact that Lip just suddenly reappeared recently in Panel de Pon DS. I think the fact that she mysteriously pops up in the same year Brawl was supposed to be released bodes well.
So anyway, Lip for Brawl!