Reeves undoubtly didn't planned everything about the sequel, but if he made Martha an Arkham and if he used all that backstory, including Elliot, there is no way to think he didn't know what to do with that.
I feel safe to exclude that HUSH in Part I was just an easter egg.
(On the contrary, I'll say that all that part - the weakest of the movie to me - was put with the specific goal to have an hook with a possible sequel: it seems quite unorganic with the rest of the plot)
I don't think Tommy will be his childhood friend (it's more likely with Harvey, it happened often in the comics but never in live action).
Personally, I think the difference with Part I will be that in the next movie, with "Bruce side" we'll se Martha pov. And consequently Arkham (and the Asylum).
Maybe it was Martha that at 15 killed her parents? Maybe that's why she was istituzionalized?
And plus, Elliot wanted to reveal ARKHAM family's secret. Not Wayne.
I think that Elliot could have been on the side of Maroni against Falcone (and so Arkham and Wayne).
I think that, as we've seen in The Penguin the Mafia side of Gotham, we'll see the noble/high society of Gotham from the pov of Bruce.
And what's so personal for Bruce won't be "a friend" from his past, but a relative (an Arkham), and the point will be "I have to save my family legacy because Nashton ruined it". But the more he will go deep in it the more it will find darkness and corruption.
I think it could be an awesome conspiracy story, I just hope as someone say it won't give the soap opera effect.
The risk is high and to me the weakest part of Part I was all the frontal talking about the past.
I have hope that Reeves took so long to write this story to improve the detective side AND to make elegant all the relevations to prevent them from the soap opera risk.