Just a quickie note/reason for why Geno may be in Mario & Luigi (bear in mind this is all speculation, as it's not like Nintendo themselves ever officially gave out a reason)
http://en.wikipedia.org/wiki/Super_Mario_RPG:_Legend_of_the_Seven_Stars
Scroll down to the Sequels section
As you can see, several Super Mario RPG employees also worked on Mario & Luigi: Super Star Saga. This includes the director (IE, the person in the highest position of the development process) Yoshihiko Maekawa, who was the director of both games. Also, the other director of SMRPG, Chihiro, at least appeared in the Special Thanks of M&L, so he likely had some influence as well. Perhaps most important is that the SMRPG character supervisor and thus one of the people most responsible for Geno's creation and also likely to be more attached to Geno as his creation, Kazuyuki Kurashima, also worked on M&L, albeit for the mini-games section. Still, the fact that he was in the staff at all means he likely had some influence.
This is confirmed by the credits to both games, here:
http://www.themushroomkingdom.net/smrpg_credits.shtml
http://www.themushroomkingdom.net/m&lss_credits.shtml
Because of this, you can't say for certain that it was initially Nintendo's own idea to put Geno in because Geno was just THAT important to them. It is at least equally plausible that it was Yoshihiko's idea or more likely, Kazuyuki's idea, and they brought it up to Nintendo and Nintendo from there decided to let them have the go-ahead. Kazuyuki Kurashima, being one of the people most responsible for Geno's design (and thus likely attached to Geno since the majority of designers love their creations if they have any soul whatsoever), could conceivably have felt guilty that Geno was stuck in third party limbo and thus requested or had the idea to include him in M&L, if only as a cameo, and brougtht that to Nintendo who would then approve.
In this scenario, Geno's "importance" to Nintendo stemming from that cameo is far less implied, as his cameo could simply have been one final tribute as a gift from Geno's creator Kazuyuki that Nintendo allowed to go ahead.
Of course, we don't know! But neither do we know that Geno was so important that Nintendo themselves screamed "We MUST have Geno in this game! He is VERY important!" and rushed to Square for it. So you can't state the latter as a fact, either. After all, it's not like Nintendo saw fit to get him to cameo again in Mario and Luigi: Partners in Time, or any other game after that.
Speaking of Partners in Time, here are the Mario & Luigi Partners in Time credits:
http://www.themushroomkingdom.net/mlpit_credits.shtml
Kazuyaki (the man who'd likely be closest to Geno) is now as absent as Geno is, although Chihiro is now moved up from Special Thanks to Field Design and Yoshihiko are still in there. This does lend a slight sliver of support to the possibility that Kazuyaki (and not Nintendo) was the primary reason for Geno being in Super Star Saga (IE, now that he's absent, Geno is gone, too.) Of course, it can't be stated for certain, but it's at least just as plausible as the idea that Geno's cameo in M&L instead means
Now, there's no reason for them to have done that if Geno is as minor and unimportant as you say. Nintendo KNOWS that Geno is a very recognizable and loved character, and his inclusion in Brawl is FAR more important than a minor cameo.