When considering which civs warrant an alternate leader, I take 3 things into account:
1. Is the current leader historically inappropriate?
2. Is the current leader's ability poorly synergized or even anti-synergistic with their respective civilization's other uniques? (I ignore weak LUAs - that's more of a holistic balance issue).
3. Disregarding 1 & 2, is there a leader that would just be cool to have even if the current leader/civ pairing is already thematic and strong?
Based off of this (and ignoring R&F civs and India), I think these are the top 4 that need an alt leader:
1. France
Catherine de Medici is both 1 and 2. She didn't lead France in life (I don't care if she was arguably the power behind the throne at times or if she was primarily responsible for navigating some tough years) and her spy-based ability, while admittedly pretty fun, doesn't tie into France's other uniques in any way. Frankly, if she made it into the game at all, it should have been as an alt leader.
While I personally love Napoleon and think having him lead his Imperial Guard would be awesome, I can't condone a militaristic France with the uniques they have; he'd have just as poor synergy as CdM even if he's a better choice historically.
I'd advocate for the return of Louis XIV. The Sun King could inject some extra oomph into a French culture game, which is what they're clearly designed to excel at even if they currently don't.
2. Egypt
I don't mind Cleopatra all that much from a historical standpoint. She did rule Egypt and even with the cultural divide between the ruling class and people, she was still fully Egyptian in my mind. Just how many centuries does a family have to rule before they're considered native to their country? You can argue she wasn't technically Egyptian, but she sure as hell wasn't fully Greek outside of her genes.
No, my reservations stem from the time period she represents more than Cleopatra herself. She was head of a Successor Kingdom dynasty that was far past its apex and on the brink of being absorbed into Rome. I'd rather see a leader from Old Egypt that represents ancient Egypt at its height. Not to mention that Mediterranean's Bride isn't a very good ability on top of a civ with abilities that are also underwhelming.
I'd like to see Ramesses II back, preferably with a LUA that interacts with Wonders and Districts in some way so that there's synergy with Iteru.
3. Spain
Philip II is historically solid. Totally deserving of his spot as Spain's leader. The problem is his LUA. While it's flavorful (heck, all of Spain's uniques are flavorful), it just works poorly with everything else. The design of Spain is too wound up with the idea of founding a religion or having a majority religion while giving you nothing special to achieve that. If you fail to snag a religion, as you very well can when playing Spain, and no one spreads one to you, most of your uniques are chucked right out the window.
For that reason and because of her continued popularity, I wouldn't mind seeing Isabella again. She could bring Spain an exploration/colonization bent that would tie in well with the Mission's newly added loyalty utility.
4. China
I'm not enough of a student of Chinese history to make specific recommendations on an appropriate alternate leader, but I do recognize the fact that China has a long and colorful history and that while Qin Shi Huang is a perfectly valid choice to lead China, there are definitely many other leaders who could tweak China's playstyle in fun and interesting ways.
Honorable Mentions (most of these are reason #3 for me)
America - No pressing need for an alternate, but I'd enjoy seeing Lincoln again or even the debut of Jefferson (we've had everyone else in the Rushmore Club at this point, plus one nephew). The former could do interesting things with Loyalty and Dark Ages while the latter could give us a scientific-leaning America.
Poland - In a hypothetical Ottoman DLC pack that didn't involve the Fall of Constantinople, it would be cool to see Jan Sobieski in a Siege of Vienna Scenario. Poland with more of a militaristic focus would be fun. After all, Golden Liberty gives you culture bombs for Encampments and Forts and converts a Military policy into a Wildcard
England - If for no other reason than she's been in every game thus far, I'd want Elizabeth again. That and she would nicely pivot England from colonial expansion to cultural refinement. Would synergize with British Museum if she had a Great Works bonus. I could see something to do with Great Works of Writing. We have leaders already that add yields to Relics, Sculptures, and Artifacts. Why not books and plays?
Germany - I'd say Frederick the Great, but we've got a Freddy already. So Otto von Bismarck, then. I'd suggest something that gives him an extra Diplomatic policy card in any government (a spin on Frederick's extra military card) plus extra loyalty for cities with two or more districts.
Civs I Don't Think Need an Alternate
Kongo - I don't think the Kongo was ever designed with an alternate leader in mind. In a vacuum, Nkisi is one of the strongest abilities in the game. It's why Religious Convert is more of a disability than ability. For balance. An alt leader for Kongo, therefore, would have a very disappointing LUA, so what's the point?
Russia - This is roughly the same situation as Kongo. Grand Embassy is pretty pathetic as far as LUAs go and it's because Mother Russia and the Lavra are so good. While I would love to see Ivan the Terrible or Catherine the Great, I feel like either of their LUAs would be terrible and not great.