Aside from the main protagonists and antagonists who appeared in the main games, but for those characters who are exclusive to MSA, I don't know if some of them are good or evil. I saw some of those character pages in Villains wiki, but not all of them are evil. Not including characters from other SNK games like King of Fighters series. Here's my thoughts.
Every member of the Regular Army are actually good.
Alice (Good) - Artificial Intellligence that was created by Marco Rossi.
Anna Wiese (Good) - One of the Regular Army private.
Midori (Good) - A rookier engineer of the Regular Army.
Perche (Good) - helped the Pengerine Falcons to defeat both Allen O Neil and Allen Jr.
Since they are the main antagonist in every games except Metal Slug 5. Most of them are EVIL especially as the main antagonist in every UNITED FRONT extra ops. Only they allies with the Regular Army temporarily in Metal Slug 3 against the Martians then in Metal Slug 6 against the Invaders. Now it's a full antagonist in Metal Slug Attack which they fought against Regular, Ptolemaics, Aliens, and Independent Armies (Except Amadeus Syndicate). None of them are redeemed or defected to their enemies.
Abigail (Evil) - She was tasked by Morden to locate Allen Jr. in the desert, but she has a crush on Trevor Spacey.
Aisha (Neutral Evil) - Another Rebel soldier who is actually personal bodyguard for Abul Abbas.
Beatriz (Evil) - Responsible for searching the Arabian Tears for Morden along with Allen Jr. Also she wants Trevor to stay out from Abigail.
Chloe (Evil) - Same motives as Rapid.
Destrade (Evil) - Originally a famed mercenary who fought for good until Allen O'Neil scouted on her.
Grazia (Evil) - Member of the Blaze Brigade.
Huracan (Neutral Good turned Evil) - Originally supposed to be an independent heroine who fend off Morden's army. Since she left her tribe, she joins the Rebel Army instead of her own. Maybe she might be redeem once if she betrayed the entire Rebel Army.
Izabella (Evil) - She likes to torture her prisoners especially Sisilia.
Julia (Evil) - Allen Jr.'s love interest.
Loretta (Evil) - Member of the Blaze Brigade and Grazia's second-in-command.
Navy (Evil) - New chief scientist of the Rebel Army since the Professor left the Rebels.
Nova (Evil) - She is actually a clone of Vita from the future.
Rapid (Evil) - Rebel Officer who is in charge in the arms supply and also a train conductor.
Shizuka (Neutral Evil) - Abul Abbas personal bodyguard.
Vita (Evil) - Rebel Army experimental soldier.
They are the original bad guys of Metal Slug 5. I'm not counting Ptolemaios as an exclusive MSA character since he first appeared in MS5 but was scrapped. However, it seems that the Ptolemaic Army would later become good since they battling against the Rebel Army as state in No Limit Extra Ops. The only Ptolemiac members who are good are those one who are loyal to their commanders and Anastasia IV(Another leader) such as Caroline, Sisilia, and Towa.
Anastasia IV (Neutral Good) - She is another leader of the Ptolemaic Army
Believers (Neutral Good)
Caroline (Neutral Evil then later Neutral Good) - Ptolemaic's mechanic who assists the Ptolemaic army with their goals. She was saved by Yoshino from Destrade in No Limit Extra Ops. In Another Story, she saves Towa from being executed. Also she appears in the Halloween another story along with Whip, Alice, and Percier.
Chunyan (Neutral Good) - Rescued by Sisilia and Veronica from a mean customer. Now she fought Amadeus along with Dragonuv and Yoshino.
Dragunov (Formerly Evil. Now Chaotic or Neutral Good) - One of the Ptolemaic Army commanders. Her goal is to obtain the "Mysterious Box" for the Ptolemaics and also attempt to execute Towa for stealing. Now she became neutral good for helping the Regular Army to defeat Morden and his army.
Miharu (Neutral Good)
Mira (Neutral Evil) - She became Ptolemeios personal bodyguard.
Owen (Neutral but bad)
Simon (Neutral Good)
Sisilia (Neutral Good) - She's just an ordinary musician and a Ptolemaic counterpart of Rumi Aikawa. Maybe she could be a Ptolemaic soldier who is actually good rather than being a bad guy unlike the rest of them.
Towa (Good) - Another mechanic of the Ptolemaic Army.
Veronica (Neutral Good) - Appears to be a young ace of the Ptolemaic Army's motorized units, but her rank is still unknown.
Yoshino (Formerly Evil. Now Chaotic or Neutral Good) - One of the Ptolemaic Army commanders. Her goal is to assist the Ptolemaic Army in conquering the world.
Annette (Neutral Good) - One of the mutant humans created by the Invaders. She's one who defeated the Cursed Ptolemaios.
Ariadna (Formerly Evil. Now Chaotic or Neutral Good) - Former Rebel Army officer who turned against Abigail.
Clone Abby (Anti-Hero) - She is a cloned mecha of Abigail that was created by the Professor in order to destroy Vita.
Clone Betty (Anti-Hero)
Fedelin Metzelei (Neutral Good)
Lydia (Unknown) - Alien invader disguised as Red Eye.
Mars People Rangers (Neutral Good)
Odette (Good) - One of the mutant humans created by the Invaders.
Percier (Neutral Good) - The Professor's lab assistant.
The Professor (Anti-Hero or Chaotic Good) - Former Rebel head scientist who betrayed the rebels. However, he only faced the PF once but later he confronts the Rebels in the Aliens Another Story.
Rillacle (Neutral Good)
Schwarz Metzelei (Chaotic Neutral)
Agilia (Neutral Good)
Aileen (Good) - She betrayed the Amadeus Syndicate and fight in her own. In the Extra Ops, she and the pirates fought the Ptolemaic Emerald Turtle.
Aswang (Good) - Originally she seeks revenge against Vatn as seen in the description. She appears to be neutral as of Another Story.
Cleopatra (Good) - Based on a real-life historical figure with the same name, she appears to be good and wanted to make the tyrant Pharaoh calm himself down.
Elena (Good) - Daughter of Red Goblin and Jin in the future.
El Dorado (Good) - He is the protector of the Sand Kingdom who protects from Abul Abbas.
Elysion (Neutral Good) - She fought the Monoeye UFO in the Extra Ops since the enemies are zombies and Rebel Walkers.
Esther (Good) - Protector of Nature against the Evil Ptolemaic Army.
Ichima (Good) - She fought along with Red Goblin in the United Front against the Martians.
Jin (Good) - Fought the Ptolemaics in the Another Story along with Red Goblin, Scotia, and Vatn.
Licht (Good) - Son of Red Goblin and Jin in the future.
Pharaoh (Neutral) - Former ruler of Egypt, but was defeated by Beatriz. Later he returns as a tyrant but later he turned back to normal by Cleopatra.
Red Goblin (Good) - The main hero of the Independent Faction who defeated Ptolemaios and the Ptolemaic Army in another story.
Scotia Amundsen (Good) - Treasure Hunter and Scott Amundsen Jr.'s daughter.
Valerian Bears (Unknown) - They never played any roles in Extra Ops or Another Story.
Vatn (Good) - Mysterious person who fought the Ptolemaics in the first independent another story.
White Baby (Evil) - Since all the Amadeus Syndicate faction are merged with the independent, she appears to be a true appearance of the white baby virus.