At first I was going to simply wrap my mind around possible 8 MK9 and 8 3D era characters, but then gave a try to guess who of the remaining characters could be a boss, which resulted in a surprising theory. Of course this is pure speculation:
MK9 8 SLOTS
-Scorpion (Confirmed)
-Sub-Zero (Confirmed. Also his undead eyes and black mask may signify the absence of Noob Saibot in the game)
-Quan Chi (Boon's favourite, and is basically a given due to his role in story)
-Raiden (Boon slipped about him far too many times. Rorschach silhouette could be a hint for hat-wearing character)
-Cage (Boon slipped about Cassie doing fatalities on family members, and having Sonya/Cassie in roster would be far more redundant than a 50-years old Van Damme)
-Cyrax (Needs at least one cyborg so that roster's diversity won't go down, and Cassie has Sektor's Up/Homing rocket already. Terminator silhouette could be a hint for cyborg character. Also was a premiere cyborg for 3D MK era. Last but not least there is unspoken rule of including at least some african-american characters, Jax is dead, Darrius was unimaginative and Kai is Nepalese)
-Ermac (a fan favourite, Boon said Scorp/Sub aren't only ninjas in game, a fanbase backlash after getting teased with that concept art only to have no Ermac at all)
I'm on the fence about last slot but should be one of these two:
-Mileena/Baraka (Needs at least one tarkatan so that roster's diversity won't go down (and I doubt a brand new tarkatan character would bring something new to the table). Barack Obama silhouette could be a hint for Baraka. Mileena is actively pushed for sex symbol of MK, and technically was sole heir to Shao Kahn's throne after MK9, however her having mind of an infant (after MK9's retcon) and absence of Kitana could limit her role to a story mode cameo instead of playable character. Hell, Kotal Kahn could just ram her with that large spear of his and become the next emperor)
MK4-DA-D-A 8 SLOTS
-Tanya (Boon's favourite aka "female scorpion" (had white eyes and fire element powers in latter installments, and yellow/black costume even before), semi-confirmed via "leak")
-Kai (White Lotus needs a representative and Kai is the first thing that comes to mind with Liu Kang/Kung Lao crossed out, plus MK team's long-time desire to give him a proper capoeira fighting style)
-Fujin (Has unique powers and MK4 portion of story obviously needs to pit Shinnok versus multiple gods, not just a single god that is Raiden, plus Fujin is possibly new Earthrealm protector after Raiden failed. Had cameo in MK9 endings)
-Reiko (Again, MK4 portion of story needs Shinnok to have a general, no reason to leave a character with established role out of it. Post-MK4 portion of story still opens for him a path to try and replace Shao Kahn. Gameplay-wise if Noob Saibot and Shao Kahn are out, that is a huge pointer to inclusion of derivation character of both of them, that is Reiko.)
-Kenshi (a huge fan favourite with appealing and unique design and powers, and was included in MK9 due to being considered BEST 3D ERA CHARACTER by MK team. He may even have more chances to be included than Ermac due to his powers being not only limited to telekinesis but also to swordsmanship and astral clones. With that in mind, he is prone to having more diverse Variations)
-Bo' Rai Cho (Boon's favourite, had cameo in MK9 endings, was always considered a very important character to storyline and heavily involved in storyline of 3D era. Again, unique powers)
-Havik (another huge fan favourite, endless storyline possibilities, unique design and unique powers, had cameo in MK9 endings, plus a sole playable representative of Chaosrealm)
-Hotaru (a counterpart to Havik, again unique design (a samurai knight in insectoid armor), personality (no one else in MK can be considered an example of
Knight Templar trope) and powers (lava, his special was given to Kintaro for MK9 now he can have it back), and best out of three playable representatives of Orderrealm)
NEWCOMERS
-D'Vorah (Confirmed)
-Ferra/Torr (Confirmed)
-Kotal Kahn (Confirmed)
-Cassie Cage (Confirmed)
-Tremor (was included in Vita and maybe this time fans bugged Boon enough for him to be included)
-new Saurian (mentioned in leak)
-a representative of Onaga's Holy Men
-logically thinking, game should have a representative of Outworld's six-limbed "sub-boss" races.
-more representatives of underdeveloped realms which are Chaosrealm/Orderrealm
-more descendants of known characters (Confirmed)
Honourable mentions:
-Liu Kang (the evil/anti-hero Liu Kang variation is likely for multiple reasons, but I feel that having him selectable right off the bat would be too easy... could be a boss or hidden character)
-Rain (Edenian story advancement due to Kitana/Jade/Sindel being dead, Boon said Scorp/Sub aren't only ninjas in game, and his power is less redundant than Ermac's - which is shared with Kenshi)
-Kano (purely due to Terminator silhouette being a possible hint to him as well, however in old storyline he was Shao Kahn/Deadly Alliance lackey at that point, so I don't see much going for him)
-Sareena (I feel like roster needs more females plus time period revolves around Netherealm invasion and all, and she is most classic/relevant out of female Brotherhood of Shadow members)
Relevance lost due to their story arc being most likely dropped:
-Armageddon/Red Dragon story arc: Mavado, Hsu Hao, Daegon, Taven, Blaze
-Deadly Alliance story arc: Li Mei, Moloch, Drahmin (even Boon confirmed that Drahmin is out)
-Black Dragon Reformed story arc: Kira, Kobra
UNPLAYABLE BOSSES
-Shinnok (A given in first part of storymode)
-Evil Raiden/Evil Liu Kang (possible BUT this is not a "surprise returning character that becomes a boss, and no one of MK fans would see it coming" that Boon was talking about - since we already had Dark Raiden/Zombie Kang in past)
-Shujinko with sub-boss Onaga (this fits the aforementioned criteria. Follow my train of thought below)
SHUJINKO THEORY
-Most people do not take this character seriously, so no one would see him as final boss
-Raiden's timeline change stuff did not cancel Shujinko's quest for Kamidogu's, and Damashi/Onaga is not influenced by that either (Deadly Alliance happening or not is not related)
-Shujinko's quest can be postponed due to new events making it harder for him to obtain Kamidogus
-If pointless "Chaosrealm aging bath" stuff is retconned, Shujinko will complete his quest and age completely later than in MKD - at the end of 25 years gap
-This is big because since Shujinko is given more time to roam around and absorb powers and abilities of EVERYONE, by the time 25 years gap ends he will become unstable due to absorbed powers, which links to his MKA ending.
-Should Onaga try and revive at that time, Shujinko will be far more powerful and thus able to one-hit kill him like Raiden killed Motaro in MK9.
-With this they can still have Onaga as MK's classic bestial sub-boss, whom Shujinko finishes in cutscene once he is defeated (much like Akuma's killing Bison to take his spot as final boss)
-The end result is, as shown in MKA ending, "went mad with power and is about to challenge the Elder Gods for control of the realms". If that's not a definition of finall boss, I don't know what is.
-A twist of having what seemed like a fundamentally good Shaolin monk-style protagonist but ended up a menace to everything, achieved.
-A nod to MK1 by having a whitebeard old master as final boss, achieved.
-A boss able to mix abilities of playable characters together and create interesting derivations, achieved. This is a simultaneous nod to MK1 final boss fight (Shang's morphs), MK4 final boss fight (Shinnok's impersonations) and SF4 boss fight (Seth)
