I am so glad to hear that the Dodongo's are going to be losing NPC faction status, as they always felt like a waste of a faction slot to me as there are far more worthy races and nations out there to make use of. Here are my comments on the five suggested replacements:
Minish - As cute as the Minish are, and as much of a challenge as they are, I just cannot see them working out, unless they make use of a lot of magic in their game (I've never played it sadly), in which case they could probably operate golems or avatars to use made from magic. To be honest though, I think the Minish should be in the game but as a merc unit for only a few factions or as part of the Kokiri (I know there is no lore connecting the Minish and Kokiri, but the Minish do only appear to children and they kinda would mesh nicely *shrugs*)
Cobble Kingdom - This is the best suggestion of the lot so far, and would bring in more from the more cartoony Zelda's which is a good thing for those of us who enjoy them. You mention them being on an island, well, if I remember correctly you have stretches of water in the north, west and south. The island could fit in any of those, and would present a worthwhile reason to get ships.
Yooks - These are one of the better suggestions, and as you said, more popular than most, although I view them as working better in a group faction rather than an NPC faction of their own. I've never been a big fan of them though, but I enjoy beating them up.
Mogma - Again, no, not a fan of those. I'm a fan of many aspects of newer Zelda's, but they aren't one of them. It'd be a waste I think, there are more worthy forces out there. I would say though, that an NPC unit would be good to see though, just not a faction.
Anouki - God no, just.. no. Never, please, never! Well, they should never be used for an NPC faction slot but they should get a single unit that can be used by rebels or as mercs, just to keep them in the lore of the game, but anymore than that is wasteful of a perfectly useful slot.
I would suggest some of my own though, ones which might work better than those already mentioned. Some are from my old "Final Collection of Races" post in the original HTW thread, whilst some are just ideas I've noticed as time has gone by. Due to us not knowing your two final factions, I am going to assume that none of those I will suggest are those two factions.
Confederacy of the Ocean King
Strengths: Cheap and effective naval forces, very diverse units to choose from
Weaknesses: Small island populations cause units to take time to produce, early game has high risk of invasion
Faction Bonuses/Penalties: None
Rival Factions: Labrynna, Hyrulean Kingdom
Cordial Factions: Tokay
Link's shifting of time has led to countless examples of the ruination of the timeline and the establishment of a more dangerous world, but there are few examples of where the corruption of time has led to the establishment of peace. As the timeline sundered, and the barriers between worlds and timestreams broke down, terrain from the future revealed itself in the present. The southern oceans of Hyrule became home to the scattered islands of the future Great Sea and of the World of the Ocean King. Long had these various islands held peace with one another, but as they emerged into this dangerous new world it became clear that peace would just not be enough, as the Labrynna Regime conquered the eastern islands. The Ocean King called upon the numerous inhabitants of the island archipelago, and managed to forge an alliance between them to protect one another against all comers.
Many know my utter love of the Wind Waker and Phantom Hourglass games, and so it should come as absolutely no surprise to anyone that one of my factions would be to do with areas associated with those games. Regardless of story or art style, the lore of the islands and races was interesting and I feel it has a true place on the Total War map. The forces of the “Confederacy of the Ocean King” would be a mishmash of different races whom have all banded together and supply a number of units for the factions unit list. The groups who would are: Hylians of Outset Isle, Humans of Windfall Isle, Rito of Dragonroost Isle, the living people of Cobble Kingdom, Pirates turned Privateers, and Koroks from the Forest Haven. The area would have a place to conquer the Yooks and Anouki that lived in those areas, as well as a few other notable islands, with the capital being on Mercay Island.
We need a faction where the navy is their greatest asset alongside trade. I feel this would provide it, and also would provide a nice bit of religion regarding the Ocean King, the Wind Gods. Who knows, even Bellum could have an impact in that region. To add these to the game in a meaningful manner, you would need to expand your map so that there is ocean that we can traverse from the north all the way down to the Tokay. Another benefit of this faction is that you will be able to build a faction out of a number of mercenary units, which means that you can gradually add to them over time as you complete the mercenary units.
Lynnian Democracy
Strengths: Some access to advanced weaponry, Goron allies provide strong infantry
Weaknesses: Advanced weaponry is expensive, as are cavalry
Faction Bonuses/Penalties: Bonus on plains
Rival Factions: Labrynna, Twili
Cordial Factions: None
Despite the originally romantic nature behind the Black Tower, the construction of it had a terrible impact upon the northern regions of Labrynna. Whilst the rich south would happily watch the construction, the poor north were those building it throughout the Endless Day, without rest and with little pay to show for it. Upon it's completion, a bitter taste was left in the mouths of the north, even moreso when the Mirror of Twilight held within it activated and spewed out the Twili. As the Twili conquered the surrounding lands in search of shards of the Mirror, the north was cut off from the influence of the south. Realising their chance, the people there rose up against Queen Ambi and established a democracy opposed to her will, even forging an alliance with the Gorons of the Rolling Ridge in the process. Though they are a rebellious force, lacking training and having few of the advanced weapons Labrynna makes use of, these downtrodden people are beginning to find their legs and establish a cultural legacy to rival their southern cousins.
Let us be honest, Total War games cannot get enough civil wars in them, and for me this could be a very interesting one. My belief is that they would have a force similar to Labrynna but with less access to gunpowder and no access to the so-called Mechs. Instead they would use the allied Gorons as their shock troops, as well as limited uses of Cavalry. I do think they would have a strong mining basis, which is something the south would lack. Not sure what else to say really, other than it'd be very cool -and- easy for UndyingNephalim to introduce.
I understand that my story description may seem out of date now but it is merely copy and pasted from my original "Final Collection of Races" post because I feel it would be a necessary faction for the eastern side of the map which is lacking in action compared to the west.
Rito
Strengths: Fast moving units, many flyers, good trade links.
Weaknesses: Poor armour, mostly skirmishing.
Faction Bonuses/Penalties: None
Rival Factions: Zora, River Zora
Cordial Factions: None
As time was ruined and the scattered remnants of time smashed together into a new timestream, one of the new arrivals in this mishmashed landscape were the Rito; a group of "birdmen" who have tales claiming that they are descendants of Zora who were uplifted by the Goddesses into a more highly evolved and sophisticated form. These new arrivals in the southern ocean have caused a stir religiously, that has brought them into conflict with many types of Zora who refute the Rito claims.
The Rito are one of the more desired factions, and would work nicely as an NPC faction in the southern Ocean, that could easily get involved in the conflicts of the east. I imagine them as being a wholly skirmishing force, which does not make them good for long drawn out melee, but they would be swift and easy to move about the map, always keeping their foes at arms length.
Gorons of Rolling Ridge
Strengths: Fast, heavy units. Very durable.
Weaknesses: High upkeep, high unit cost, slow.
Faction Bonuses/Penalties: Bonus in Desert, Penalty for Snow
Rival Factions: Labrynna Regime
Cordial Factions: Fairies of Tarm, Holodron
To the north of Labrynna are the long suffering Goron Tribes, these Goron have long been used by Labrynna as underpaid work or as slaves, and the fumes of Labrynnan industry have begun to make a severe impact upon the Goron lands and upon them as well. In the face of this new danger to their lands, the various tribes of have banded together and collectively come to name their lands as The Rolling Ridge, who stand ready now to repel the ever expanding industry of Labrynna and forge their own future as rulers instead of as slaves.
I feel Labrynna needs more foes, and a Rolling Ridge NPC faction would provide this. If I was to add these Goron, I would make them of a different ethnicity to the Goron faction in game, probably by making them a slimmer and darker skinned version. They do not need many units, but I feel that any they do have should have a unique style to their armour and weapons, to make them differ more with their western cousins.
Pirates of the Great Bay
Strengths: Good navy, good archers, good movement
Weaknesses: lacking in armour, lacking in allies
Faction Bonuses/Penalties: None
Rival Factions: Labrynna Regime, Tokay
Cordial Factions: None
The Gerudo have long suffered in the merciless deserts to the west of Hyrule, and most have been too stubborn to move on from those lands to find a more plentiful home to settle, or merely incapable. Over the past few centuries, however, a number of Gerudo have taken to travelling towards the south-east, where they have established a town on the coast of the Southern Seas. Although the intentions of the original settlers were wholly good, they soon realised that they had no decent knowledge of how to grow crops in fertile lands or how to fish from the oceans, and soon the settlers took to piracy to gain coin and resources to survive. The Gerudo Pirates of the Great Bay are one of the great threats to the stability of the south, and year by year their influence is growing, enough so that their Pirate Queen is even beginning to threaten Labrynna.
A lot of followers of this mod are also big fans of Majora's Mask and Termina in general, this faction is a nod to them, by adding in the Gerudo Pirates but in a way which does not mash Hyrule and Termina together. Also, as a fan of the ocean-going Wind Waker game, I have been saddened at the lack of support for the oceans and the lack of Pirates in the game, thus this faction would cure that. Also, the units for this faction would be distinctive compared to other Human forces (due to piratey-ness) but also relatively easy compared to making a faction of some new species.