Some ideas?

[Vlado87]

IDEA 1:
After clone war we can see CIS holdouts (similarly to imperial warlords and imperial civil war).

So in Fall of Republic we can see next "eras":
era 1 clone war - Republic VS Confederate
era 2 something between clone war and civil war - Empire (with late republic fleet / army and some early imperial fleet / army) VS CIS holdouts
era 3 early civil war - empire VS Rebels, CIS holdouts

IDEA 2:
In clone war when you play as Republic you progress through eras when you kill some CIS leaders.
When you play as CIS you progress through eras when you kill some Republic leaders.

IDEA 3:
When player kill some super heroes or leaders than player have access to some special ships or units.

For republic this can be: legacy venator destroyer (upgraded venator), mandator MK II, Imperial star destroyer, invisible dreadnought, Legator star drednought (from fractalsponge),  Secutor star destroyer (version with venator bridge)

For CIS this can be:  kandosii dreadnought, crescent star cruiser, upgraded Harrower dreadnought MK II (after CIS victory in Battle for Coruscant from film), Dreadnaught heavy cruiser, Subjugator heavy destroyer (malevolence without ion super weapon) and Providence carrier destroyer (in beginning player will have this ship only as hero ships (trench, invisible hand, colicoid swarm, lucid voice) but after CIS kill some Republic hero than CIS will have this ship for normal build).

[Bucman55]

IDEA 1:
I seem to remember Corey saying they wouldn't go into the early Imperial period (at least, in the initial release) but I can't remember where he said it (if he said it).

IDEA 2:
"The leader-based era-system in ICW works because of the nature of the time period. There are some fairly distinct regimes within the Empire, with events that dictated how the galaxy was operating during those regimes. The FotR period doesn't really have cleavages in the same way. It has other options. And while there will likely be some aspect of research in it, like what we're doing with the NR in 2.2, it won't be the traditional kind of "Tech level 1 you only get corvettes" thing. The feeling should be a lot closer to Imperial Civil War. Given sufficient resources, there are other ways I'd like it to resemble Imperial Civil War as well." - Corey ( http://thrawnsrevenge.com/forums/index.php?topic=6567.0 )

IDEA 3:
I don't know about this.

The "Legacy Venator Destroyer" is not a real ship, the Mandator II could make an appearance, ditto on the ISD I, I have my doubts the Republic would make use of the Invincible-Class Dreadnaught, the Legator does not exist, and as far as we know, the Secutor was not designed yet.

The Kandosii Dreadnought was not used by the CIS in any capacity (in fact there is no record of anybody using them past the end of the Mandalorian Wars, Is this what you are referring to? The Harrower was not used by the CIS in any capacity (wouldn't make sense anyway), maybe on the Dreadnaught (possibly if Rendili is taken), the Subjugator and Providence will likely be standard buildable units for the CIS.

[Vlado87]

http://starwars-exodus.wikia.com/wiki/Crescent-class_Star_Cruiser

Well in canon Clone wars some of those ships was not used by Republic or CIS but in canon CW CIS was not conquer Mandalor so they are not have access to mandalorian ships, similar with the Harrower if CIS win in Battle for Coruscant than Sith lord will give access to CIS for building Harrower, there are only two Subjugator ships in canon Malevolence  and Devastation
http://starwars.wikia.com/wiki/Malevolence
http://starwars.wikia.com/wiki/Devastation
but I think that would be nice to see both of those ships but it would be nice to see third version (this is not canon), if is dead Anakin S., Palpatin and Obi One and if CIS have access to Calamari Moon  than General Grievous can build third version of subjugator and this ship will have only standard weapons (normal lasers and normal ion weapons) not some super weapon that would be Malevolence without those super ion weapon.

I want to say what if CIS conquer Mandalor or they win in Battle for Coruscant or Anakin and Obi One was killed or they conquer Calamari Moon or what if Rendili is conquered in those cases CIS must have access to some new tehnology
and same with Republic in beggining they should have one invisible dreadnought (with new weapon) and it is not buildable more of them but when CIS destroy this ship than Republic can build on Kuat Mandator MKI dreadnought after this ship is destroyed than can be build Mandator MKII dreadnought and if Republic lose Battle for Coruscant and if in battle was killed Anakin and Obi One then Republic should have access to one legator star dreadnought.

There have not be those ships what I am write but must be some ways to access some new and special.

[Bucman55]

http://starwars-exodus.wikia.com/wiki/Crescent-class_Star_Cruiser

I'm pretty sure that ship does not exist within the Official Legends timeline.

Well in canon Clone wars some of those ships was not used by Republic or CIS but in canon CW CIS was not conquer Mandalor so they are not have access to mandalorian ships...

The reason they didn't have access to Mandalorian ships was because there were no mandalorian ships to access. All of the Mandalorian warship designs were well over 3,000 years old, thus making them extremely outdated compared to modern designs.

...similar with the Harrower if CIS win in Battle for Coruscant than Sith lord will give access to CIS for building Harrower...

The CIS wouldn't have been able to get Harrowers even if they wanted to. The CIS showed no interest in using ships that were over 3,000 years old.

...there are only two Subjugator ships in canon Malevolence  and Devastation...

Actually, if you look at all of Legends there were at least 5 Subjugator-Class Heavy Cruisers that were used by the CIS (Subjugator, Malevolence, Devastation, Malevolence II, Unidentified).

but I think that would be nice to see both of those ships but it would be nice to see third version (this is not canon), if is dead Anakin S., Palpatin and Obi One and if CIS have access to Calamari Moon  than General Grievous can build third version of subjugator and this ship will have only standard weapons (normal lasers and normal ion weapons) not some super weapon that would be Malevolence without those super ion weapon.

I can't speak for the team as I have no idea what they plan to do (neither do they at this point, if what Corey says regarding FotR is accurate) but I would assume the CIS would be able to build Subjugators like the IR can build Executors. The Subjugator was one such cruiser without any of the super-weapons. It was instead armed with a Trihexalon Launcher, alongside the standard armament for a Subjugator-Class.

I want to say what if CIS conquer Mandalore or they win in Battle for Coruscant or Anakin and Obi-Wan was killed or they conquer Calamari Moon or what if Rendili is conquered in those cases CIS must have access to some new tehnology...

If the CIS were to gain control of any of those planets, they probably would have continued to produce their own units. They might make use of captured vessels, but they likely wouldn't produce more of them.

...same with Republic in beginning they should have one Invincible-Class Dreadnaught (with new weapon) and it is not buildable more of them but when CIS destroy this ship than Republic can build on Kuat Mandator MKI dreadnought after this ship is destroyed than can be build Mandator MKII dreadnought and if Republic lose Battle for Coruscant and if in battle was killed Anakin and Obi-Wan then Republic should have access to one legator star dreadnought.

The Republic did not have any Invincible-Class Dreadnaughts in their Navy at the time of the Clone Wars. Those ships were most likely decommissioned well before the beginning of the Stark Hyperspace War due to the Republic's decision to de-militarize. The Republic could build Mandators like the IR builds Executors in ICW, and Legators are not real ships.