Not every set needs to have multiple villains. Is it a fun inclusion? Yeah sure, but I would rather have a better looking model than some random D-list supervillain that somehow was glanced over whilst creating the CMF series and the other sets. I'll kinda sorta agree with you when it comes to the penguins. Although they were included in this line's Batcave, seeing at least one would've been nice.
I personally prefer the shorter back. It makes the front more pronounced, making it feel somewhat longer than it really is.
The six wheel design is arguably a better move. The giant tires in the front wouldn't compliment the back very well. If they were to use the smaller wheel, it would make the back look a bit boring.