Emperor: Battle For Dune.
An old RTS created by Westwood Studios known for their C&C series. E:BFD has gameplay quite similar to C&C (MCVs, Construction Yards, Harvesters, side panel that allows you to manage reinforcement creation without taking attention off the battle), together with Dune-typical living world (Sand Worms, whirlwinds, etc). Has three factions and several subfactions which you can ally in during skirmish/campaign. Campaign requires you to play loyality missions for these subfactions and places several limitations. In skirmish you can ally two of any subfactions.
The campaign offers a strategic map of sorts in an attempt to make things non-linear, but there still are several plot-required missions. So far I have finished Harkonnen campaign (twice) and reached last mission as Ordos.
(Note that I didn't really learn absolutely everything, I am just relaying my experiences. Feel free to bash them down and then make Gholas out of them just to bash them more as you see fit).
Three main factions are the noble House Atreides, the plotting House Ordos and capital E Evil House Harkonnen.
House Atreides are Balanced. They have decent infantry, snipers capable of taking out enemy infantry at range and Kindjal Infantry armed with a man-portable anti-tank cannon. Their vehicles are decent too, their MBT analogue the Mongoose walker can attack air targets, Minotaur walker is a powerful artillery vehicle and Sonic Tanks can deal a lot of damage to anything they catch in their way. Their superweapon is Hawk Strike, which causes all units in target area to flee the operational area.
(Turns out the effect of Hawk Strike is permanent against Harkonnen Air Defense Platforms. I ended up simply force-killing those affected with Missile Tanks because flak them.)
However, they have no AA capable infantry.
House Ordos are Subversive. Instead of an assault rifle, their basic infantryman is armed with a chemical sprayer. They also have Mortar Soldiers and Saboteur suicide bomber. Their MBT, APC and Deviators are hover, shielded vehicles capable of traversing dustbowls (but incapable of crushing infantry). However, when a shielded vehicle is hit by a laser weapon, both units are instantly destroyed - and Ordos MBT is armed with a laser.
(Imperial Sardaukar Elites also carry laser pistols which have the same effect).
Deviator is the Ordos' star player. It can temporarily switch a vehicle's allegiance to you. Particularly effective against Harkonnen Devastators.
All their combat vehicles have regenerating hitpoints. It also applies to Ordos Dust Scout and Kobra Unit, which deserves a separate mention - it is essentially a Siege Tank, a dual-mode unit armed with an artillery howitzer.
They don't have a traditional attack aircraft, instead, they have Eye In The Sky, which can detonate, dropping down several charges and its Saboteur pilot.
Their superweapon is Chaos Lightning. It causes affected units to attack anything they think is moving.
House Harkonnen are the Powerhouse. They lack APCs, but have more to offer. Their scout vehicle the Buzzsaw can crush infantry and destroy any spice it passes over, potentially leading to Scorched Earth warfare. For more infantry hate HKs have Flame Tanks and Flamethrower Infantry, and to some degree their artillery unit the Inkvine Catapult. The Catapult has slow projectile speed, but also causes damage over time to infantry in the area of impact. The Missile Tank also deserves a mention, since it deals tremendous damage in a single salvo yet has long reload time, and it can attack air targets.
The Harkonnen Devastator is their star player, best friend of Ordos Deviators and favorite snack of the Sand Worm. Slow as molasses and heavily armored, it is armed with two plasma cannons and AG/AA missile launcher. If you see fit you can order it to self-destruct, causing a large explosion. Best results can be achieved in combination with an Advanced Carryall.
Another thing of note is Harkonnen Air Defense Platform. All houses have an air-to-air unit (Atreides Air Drone, Ordos AA Mine and HKADP), but Air Defense Platform can turn its quad autocannon against land units. Only thing preventing HKADP from becoming imba is that they are very fragile, but there are precious little that can target them.
Harkonnen Superweapon is Death Hand Missile. It deals high damage and leaves a large damage over time area.
The subfactions are Sardaukar, Fremen, Ix, Tleilaxu and the Spacing Guild. Each offer a pair of units. Sardaukar have powerful shock trooper infantry, Sardaukar and Sardaukar Elites. The latter can attack air units with laser pistols and instantly kill infantry with their knives. Fremen offer stealth infantry, Warriors (snipers) and Fedaykin (armed with sonic pistols). Ix have Infiltrators, stealthed suicide bombers capable of revealing stealth units, and Projectors, hover tanks armed with autocannons that can deploy into duplication mode. In duplication mode they can create duplicates of units. The duplicates will disappear from the smallest damage or contact with any enemy unit, but any damage they cause is pretty much real. I learned to use duplicates of Harkonnen Missile Tanks as cruise missile: set target, watch the duplicate scrap it with the missile salvo and you don't care if it doesn't live to launch a second one. Tleilaxu offer Contaminators and Leeches. Contaminators turn any trooper they kill into additional contaminators, Leeches can infect a vehicle that upon destruction releases another Leech (unless saved by an Engineer). Faced with either infantry or vehicles, a Tleilaxu army has a potential to multiply. Guild offers Guild Makers - I didn't quite catch what they do - and NIAB tanks, which can teleport short distances.
In campaign, Sardaukar and Fremen are enemies, so are Ix and Tleilaxu, Fremen won't ally to House Harkonnen and Guild isn't present at all.
Until the final mission, that is. Tleilaxu and the Guild betray you and hatch their own plans to seize control of Arrakis. Sardaukar, Fremen and Ix, on learning of this, ally with the player's house, which ends up becoming Arrakis's - and the galaxy's - only hope. Which becomes hilarious if said house is House Harkonnen.
The soundtrack deserves a separate mention. Each side has its own set of tracks. Atreides boasts rock soundtrack with arabic/space motives, courtesy of Frank Klepacki (composer of most of C&C OST, Act on Instinct and Hell March in particular). Ordos have weird electronic tracks by Jarrid Mendelson (composer of several tracks from C&C Tiberian Sun, such as Lone Trooper). Harkonnen themes are pure metal by David Arkenstone.