Alrighty, time for my own list.
Characters (2):
The entire cast could be playable and would work really well, but I think more than two is unnecessary at this point. After we revitalize the series and get a few more games in, we can work on building character representation. I'd go with Isaac and Jenna. Two great characters, both with really unique playstyles. Plus, Jenna's unique Psynergies would help her stand out more than any other Fire Adept we might get in the game.
Stages (4):
Sol Sanctum and the Lighthouse Aerie (Wii U). Both good stages with excellent stage hazards. The Lighthouse Aerie would change up which lighthouse it was, split open to reveal the elemental beacon, and of course have the effects of the beacon itself. Sol Sanctum would have the changing Sun/Moon logo leading to the volcanic eruption and collapse.
Endless Wall and Air's Rock (3DS). I like the idea of Endless Wall as a relatively simple, walk-off stage. However, this is during the Grave Eclipse, so there are a lot of baddies around as stage hazards. Plus, I think it would actually be a travelling walk-off, going along the length, until it reaches the Apollo Lens, which will then fire. Air's Rock is just such a well-known location. For only a minor stop on the journey you wind up spending quite a bit of time there (especially on your first run through), and it really sticks in the mind. Tons of wind gusts blowing that make for interesting traversal across the platforms, and some really clever recovery options.
Assist Trophies (4):
Sage Hama. Because she's awesome. The Colosso Trio. Because they think they're awesome, and I can totally see them challenging Smash fighters for a short time before realizing they're outclassed and running away. Alex. Because he is a helpful character who fights alongside the party at times, and would be really fun and easy to implement. The Wise One. Do not mess with the floating rock.
Items (4):
Djinn. One of each element. You pick them up, and they're basically Mr. Saturn. But, when you throw them, they hit a person, then a few seconds later they attack with their element. Earth uses Bramble or Gaia. Water uses Douse or Prism. Wind uses Plasma or Whirlwind. Fire uses Eruption or Flare.
Music (6):
Isaac's theme. Jenna's theme. Mars Lighthouse theme. Battle Against Saturos/Star Magician theme. Doom Dragon theme. Fusion Dragon/Dullahan theme.