I really hope one day the Doctor bumps back into some of the kids from SJA. They're all still acting, all in their 20s. I always thought Clyde was the greatest companion the Doctor never had of the recent era - something which comes through in his interactions with Tennant and Smith in the episodes they appeared in. I think eventually we will reach the time when the Liz wounds aren't so raw that we can have Luke appear and reveal that in-universe Sarah Jane has passed on. Give her a goodbye. Maybe he'll be the Kate Stewart figure in 20 years' time, heh.
To be fair to what you are saying, you could have removed Jack, Sarah Jane and Martha Jones from the whole script and barely any of the episode would have changed. The only important players in the episode were Rose, Donna and the Doctor. Everyone else was plot fluff.
I honestly disagree with this as Jack has a clear role - like in Series 1's finale, he's there to be the one willing to commit violence. An enormous part of the emotional point of the whole episode is when he and Sarah Jane - two unlikely allies, given the antithesis of what their two shows are about - team up, his know how, her technology, the plan literally to perform a suicide bombing. The episode needed that beat, and so Jack and Sarah are actually pretty key in an emotional sense, if not in a plot nuts-and-bolts thing.
Jackie and Mickey don't have anything to do, though, and it's clear RTD struggled - in the writers' tale he talks about removing Jackie from the script, but laments that they'd already booked Camille Coduri for the weeks and he went back and forth about just having her on Bad Wolf Bay at the end, but then kept her in throughout. Mickey I think fits as good window-dressing - there's a good dynamic between him and Jack, and there was a real-world reason for putting him in because at the time the plan was for him to join Torchwood full-time... then his directing career took off and that killed that idea, but still.
Martha, however - I think she belongs, but I do think Journey's End shows, for better and for worse, how she's the odd one out. Everyone else is interacting all the time. The show goes to pains to put all of the 'true' companions together by the end of part one - Rose, Jack, Donna and the Doctor, together in the TARDIS. Martha is left behind. It takes care to give Jack and Sarah scenes together, to stitch Torchwood and SJA together. Jack and Mickey have a great relationship. But it's strange, honestly - like Jack and Martha don't interact one-on-one at all really, something strange considering she's actually been a temporary member of the Torchwood team at that point.
Even towards the end - everyone is sort of pairing off as the Dalek plan backfires. Donna and the two Doctors are together, doing the work. But then you get shots of people teaming up - Jack tossing Mickey a gun and the pair of them holding up Davros, Sarah and Rose greeting each other while pushing away a helpless Dalek. Martha gets a shot on her own.
She doesn't fit with the group. (Though she fits in the episode for similar reasons to Jack/Sarah). She never did. But that, I suppose, is in many ways the point of her character.
