What makes BB and TDK head and shoulders above the rest of the Batman franchise and most other superhero movies is that Bruce is a developing character and he has a strong through-line in each movie.
See, I didn't think Bruce really had a character arc in TDK. He really seemed like a side character with more emphasis on what the Joker and Harvey Dent were up to. The only change the character went through was the out-of-nowhere decision to take the fall for all the murders Harvey did.
The villain that rises for him to deal with is Rupert Thorne, a true corrupt, corporate monster, more subtle than any mobster, with deep ties into the city and state, even federal government, and Wayne's equal socially, financially and in terms of intelligence. The kind of guy who works entirely through fronts (so you can have whichever of the traditional villains you want - Riddler, Deadshot, Catwoman, Poison Ivy, whatever, and only reveal him as the ultimate villain in the second half) and who, when Batman confronts him with a list of his crimes can merely smile and say, "Oh yeah? Prove it."
If they do Thorne, I say keep him as a congressman like in the comics. The way you describe him there makes him sound too much like Lex Luthor. Also, I am pretty sure Bats (at least this version of him) would come at him with the proof.
Actually having him as a congressman would work great since Bats is on the run. A politician would totally take advantage of that.
I still think Penguin could be worked in there as the new Mob boss, but not nearly as bad as the previous mob bosses. My favorite bits in the comics is when Batman pumps Penguin for info in exchange for looking the other way on things.
[...] now that Lucious has cut himself off from aiding him because of the actions with the cell [...]
No, they are still on good terms. Lucius didn't like the device and swore to not work at Wayne enterprises as long as that thing is there, which is why Bruce made Lucius the only one to operate it (and subsequently destroy it after he typed his name into it). I think their relationship is just fine.
That being said, what completely ridiculous device should a third Batman movie have? The first two had them, so we need one for the third movie!
