(this is really a repetition of what the guide's info says)

What is this about? It's a quick summary of how certain civs can be played in lore-friendly games, but using them in a slightly different way than what they were meant to represent. Primarily, my scope is to make certain civs "usable" as "good guys" (i.e. enemies of the Galactic Empire), by referencing the lore. This of course, allows for more civ variety for those who want to use a civ for their mechanics and features, but not for their primary allegiance.

To further clarify with an example, a game where the Trade Federation and Rebel Alliance stand allied against the Galactic Empire would naturally not be lore-friendly, and you'd rather imagine the TF in a face-off with the Republic or the Wookies, but in reality this is totally lore-friendly. I'll show you how.

These two civilisations can both be used as allies of the Rebels and/or enemies of the Empire.

Both factions, during the early Imperial Era, struggled to survive against the Empire's suppression. In this context they can be used merely as enemy of the Empire.

By going a bit forward in time, toward the last few years preceding the Battle of Yavin, the so-called "Separatist Holdouts" began merging into the Rebel Alliance and thus effectively fought the Empire using what droid and mech armies they could muster. This is true for both the 'successors' of the Confederate worlds and those of the Trade Federation.

Reference pages:
https://starwars.fandom.com/wiki/B2_super_battle_droid/Legends#Post-Clone_Wars
https://starwars.fandom.com/wiki/Separatist_holdouts/Legends#The_Alliance_and_Separatism
https://static.wikia.nocookie.net/starwars/images/6/66/Rebels_and_droids_vs_Imperials.png/revision/latest?cb=20161024195842

Note that most of the factories which produced the droid armies were shut down or absorbed by the Empire. War droids were declared illegal by the GE and so were not produced at all. I cannot find anything proving the above factions managed to restore an actual production of war droids, so all of those which were used were found/scavenged/repaired. This means their numbers were smaller, and separatist remnants fought in person (with organic troops) much more often.
Concerning vehicles, I didn't look too much into it, but it seems there is little to be read about it. It is likely that the resources of the Separatist remnants were limited and allowed for few mechs to be deployed.

This issue and that of the droids can be remedied, if one really feels like being super lore-friendly, by playing against a very hard AI Galactic Empire, allied with several factions (civs) which united under the Rebel Alliance. Note that your only lore-friendly enemy would be the Galactic Empire in this time period anyway. Last of all, if you want to portray an increased use of organics, train a lot of bounty hunters. Sure, they are expensive, but all can be sacrificed for the sake of accuracy eh? lol

You can use the Galactic Empire civ as an ally of the rebels if you mean to portray a sub-group of imperial defectors. I personally don't see this as making too much sense, but yes the Rebel Alliance was full of Imperial defectors and I imagine they brought in plenty of men, equipment and some vehicles, as a few were high ranking. See here for yourself:

https://starwars.fandom.com/wiki/Category:Imperial_defectors

Of course, as with the other civs described in this guide, you should not use Sith units. This can be more complicated when playing as the GE as it is balanced to be using Siths, unlike the Confederacy and the TF which can really not use them at all.

Unfortunately, the Republic can only be used effectively in the small time-frame of the Clone Wars, if you want to stay lore-friendly. Rebel armies were radically different from the Clone Army seen in-game. If anything, the Republic as a civ can more realistically be used as an early Empire.

There were also no battalions of clone troopers which defected for a time and put up a resistance against their former brethren (the newly formed stormtroopers). There is only one very small case of a squad of troopers refusing to kill their jedi general, but we are talking of a 5 or 6 men squad. Not really a faction at all.

The only credible instance you could exploit would be this remnant of the Republic Army (https://starwars.fandom.com/wiki/Kota%27s_Militia) which survived the Empire's suppression and managed to unite with the rebel alliance - however they were not clones, which is why they resisted, and thus appear to match little with the Republic civ as it is portrayed in-game.

It is true that Rebel spec-ops infantry wore full body armor akin to that of the Republic's or the Empire's troopers. (reference: https://starwars.fandom.com/wiki/Alliance_Special_Operations)
This could be another idea. However, the heavy reliance on Jedis the Republic civ features, makes it nearly impossible to be used that way. I just inserted this section to write down the result of the research I made and to give a couple of little-viable ideas for those really interested in using the Republic against the Empire.

Royal Naboo saw little participation in the Galactic Civil War, and as a matter of fact the civ in-game is meant to portray primarily if not solely, the Clone Wars-era Naboo.

However, Royal Naboo forces actually did wage war against the Empire and drove off the Imperials together with the Gungans. Conversely, you could also use Royal Naboo as an Imperial 'ally'. For whatever reason, Naboo maintained some degree of independence and the Empire never fully abolished its monarchy, preferring to set up puppet rulers (and often failing to do so).

See the detailed story/lore here for both instances: https://starwars.fandom.com/wiki/Naboo/Legends#Imperial_period

Concerning the Gungans, see what is cited above. They were not wiped out and did contribute to driving off the Imperial forces from Naboo.