Also, while I'm at it with SMM2 speculation...
Fuzzy and Swoop would be easy to include, and I expect that these two enemies will make it in at some point during SMM2's lifetime. They may not have many interactions, but they're 2D Mario staples nonetheless. Enemies like the Chargin' Chuck, who I also believe will make it over at some point, will be much more difficult to include. Only two variants of the 7 though; a standard and an alt. Chargin' and Jumpin' make the most sense. The Fire Snake and Flame Chomp are recurring enemies, but have different variations and interactions, so I'm not sold on them yet. They make sense as 4th and 5th picks.
However, I feel like the water will receive the largest content boost with Version 3. From the Spiny Cheep Cheep / Rip Van Fish (or whatever they decide to call that blue homing cheep cheep), to the Urchin or Porcupuffer, this is the theme that is lacking the most specific enemies.
On that note, there will probably be two more themes coming too, being the Beach and Volcano. Both of these themes would supply the theme-pool with another level for liquid adjusting, and about time too. Castles can't be the only source of lava, and can take away from the true hectic experience of a vertical rising-lava stage (imo). Beaches have the same accord. The water in the NSMBU Jungle is kind of off-putting, after playing NSMBU and knowing that water never appears with that theme. A night-time variant can have the liquids be upside-down for both themes. Interesting stuff, unless you're in the camp for meteors on a night-time Volcano.
Honorable mentions for themes go to... Mountain. Sadly, there isn't that much special about the Mountain theme, unless you want to complete the set of themes from the New Soup games.
Oh yeah, and the honorable mentions for enemies go to the Mechakoopa and Blargg, for existing and actually having some notability in 2D Mario circles.
A Scuttlebug would be cool as heck but obviously isn't coming.
Why do I sound like a conspiracy theorist? I'm not even going to cover potential power-ups or gamemodes because I sound crazy already.