Here's one very important thing to consider: when choosing a character for the last slots, it's not just about what you want (which is what this poll shows), it's also what is easiest for the PMBR. You basically don't like the concept of a clone character (and as DatDolphin pointed out, we already have quite a few already), but here are some key one points about clones:
1. The PMBR is not Sakurai. They don't have god powers that create characters from scratch. Many of these characters, like Isaac, are presented as if they were to be from scratch. There are many, many limitations. Clone characters do not have these limitations.
2. Animations: These are probably the most time-consuming thing. New characters will need a ton of time for new animations. Clone characters reuse animations. Maybe a few moves or walking/running animations can be edited, but not the whole character. Huge burden reduced.
3. Movesets: There are actually TWO factors with movesets: 1) Coming up with one -- which again, is minimized with clone characters -- you just change parameters and change 1-2 few moves. 2) Balance. People are familiar with these movesets that have been used for years. Creating a new one from scratch not only takes a lot of time to create, but it may take even longer to balance. If a moveset is based on an old one, balance will still need a lot of time, but considerably less compared to a novel moveset.
With so many restraints, the PMBR will undoubtedly have clone characters. They even said that's ideal in their post. Maybe even all the new characters would be clones.
So maybe you don't like Dark Samus, but when we have to choose characters that are clones, she is one of the better choices. The fact that the character can be implemented AS one is may seem like a big con for you, but it's a tremendous pro to the PMBR.