On one side of the war, we have the Masters. The modern-day magi that fight tooth and nail for a chance at the Holy Grail. On the other side, we have the Servants. Their famous familiars and (sometimes) faithful Servants with awesome power thanks to their grand legends. We may know how the 4th Holy Grail War ended up but what would happen if we mixed things up.
What follows is a what-if scenario for the ages! Taking the Masters and the Servants, we mix and match them to see how the new combinations would fare and how it would affect the outcome of the whole Grail War. Welcome to Fate/Zero: Alternative Edition.
8 Kotomine & Gilgamesh
Some people might consider this cheating and but we consider this cutting the middle-man out. (Just like Kotomine did.) Now instead of stealing Gilgamesh out from under the dead body of Tokiomi, Kotomine was lucky enough to have summoned Gilgamesh from the get-go.
With this small change, there wouldn't be too many differences between them. They would still start forced allies and then become accomplices in the crusade to make each other's true intentions come true. Gilgamesh would once again usher out Kotomine's bad side and Kotomine would help Gilgamesh in getting the Grail. The only difference would be that Tokiomi might get to live a bit longer.
7 Tokiomi & Saber
Tokiomi does what his daughter could not, successfully summon Saber. If Rin could gather the necessary components to summon Saber in a time when the Tohsaka family was struggling then Tokiomi should have no problem doing the same back in its prime.
How'd they would get along... that is another matter. While Tokiomi doesn't flaunt it as openly as Kiritsugu and his "blow up a hotel to get one mage" lifestyle, Tokiomi would do nearly anything to get results. This is the man who pawned off his own daughter to another family to make sure Sakura and Rin didn't fight over being the heir, so its a safe bet to believe he would be willing to bend the rules to get a good result. And if that doesn't piss her off, having to work with Gilgamesh and Kotomine would. At least, until the inevitable backstab.
The only question left would be if Saber was enough to protect him?
6 Kayneth & Rider
Let's say that Kayneth's original catalyst wasn't stolen by Waver and he managed to summon Alexander the Great as intended. How would that turn out? Probably pretty complicated.
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While Rider would admire Kayneth's wish to have a proper mage battle, his tendency to hide behind his Servant would grate at his nerves. Waver was nowhere near as talented as Kayneth when it came to magic, but Rider admired that Waver was willing to stand beside him in battle. Much like his soldiers did when he lived. At the very least, Kayneth wouldn't have to deal with Lancer's magical enchantment that made his fiance fall in love with his Servant.
5 Waver & Lancer
Oh! No! Waver stole the wrong catalyst! Whatever will he do? Pretty well, actually.
While Lancer doesn't have the same mentor vibe that Rider had, he would still treat Waver like a little brother. The bond would be different, but it would still be there as the loyal knight would take care of his young charge. There would be quite a few bumps in the road due to Waver's tendencies to act like a spoiled child, but Lancer's loyalty would probably serve to help even him out. Giving him much needed confidence and a sense of self-worth.
There is a chance that Lancer would get something out of this too. If they managed to meet Saber by herself, there is the possibility that he would manage to get a proper fight with her like he always wanted. As long as Tokiomi, Kotomine, or Gilgamesh don't get in their way.
4 Ryuunosuke & Assassin
A killer with a killer. While Ryuunosuke and Assassin wouldn't bond on the same level as he did with Caster, he would still try to make great use of the great killer. Ryuunosuke is an unrepentant madman and would delight at the chance to have a small army of trained killers to do his bidding. Probably immediately putting them to work to further learn everything he can about death. Turning his already horrible killing spree into a full-on massacre. Leading to the first great crisis in the Grail War.
Much like with Caster, he would cause a giant problem that all participants would need to deal with. With a killer and his Servant having their merry way with the people of Fuyuki city, the supervisor in charge would task the other Masters and Servants with killing them. That amount of carnage enough to threaten the Holy Grail War and the secrecy between magi and the general public.
3 Kariya & Caster
Poor, Kariya. He didn't have much luck in the Fate/Zero and this alternative take wouldn't be much better for him. In the same spirit of suffering, Zouken would push Kariya towards a despicable Servant like Caster and then Caster would probably take advantage of Kariya's weakened mind and body to corrupt him. Much like Gilles De Rais lost his mind after Jeanne d'Arc was burnt at the stake, so to would Kariya consider darker means if Sakura was on the line
In the end, Caster would probably lead the beat up and mentally not-all-there Kariya by the nose for the entire Grail War. Delighting in all of the wonderful atrocities he could commit all while promising that it was all in an attempt to help him save Sakura. Eventually, leading to a similar conclusion. He would try to summon a dark god and the other Servants would try to stop him. Kariya probably doing no better in the end with Caster by his side.
2 Kiritsugu & Berserker
The only problem with this set-up is that Kerry is a great mage killer but a horrible mage. Kiritugu doesn't have the magical power to properly supplement Berserker Servants who are like open facets when it comes to mana consumption. Thankfully, that is a pretty easy fix and her name is Irisviel.
Just like her daughter, Irisviel can become a Holy Grail... though to a less refined extent. That should give her enough magical capacity to handle a Berserker class if she were to do the same thing Sola-Ui did for Kayneth. Thankfully, Lancelot's mana consumption is less than the amount Heracles requires, so she should be able to handle it just fine. This should give Kiritsugu a wild but loyal lapdog to do his bidding.
And that would work for a time until she runs into Kotomine and he stabs her in the stomach. Without the power of Avalon and Saber to support her, she would die from her injuries. This leaves Kiritsugu with a Servant he can no longer maintain. This means he would either have to watch Berserker fade away or die with him as Berserker drains his mana dry.
1 The Winner: Kotomine & Gilgamesh
Without the standard set of Servants and Masters in this Grail war, Kotomine and Gilgamesh are too powerful not to win. The only other combo that would come close would be Kotomine and Berserker and Tokiomi and Saber in this alternative take. Even then, Berserker and Saber are just not strong enough to take on Gilgamesh without some help or special circumstance. Especially since the thought of them working together is non-existent.
The other sets do not stand a match. Gilgamesh could easily conquer Assassin and Caster in the same fight. The Knight of Fiona and Rider would put up a valiant effort but they too would succumb under the weight of hundreds of weapons being flung their way. Kiritsugu could attempt to assassinate Kotomine, but that rotten priest has too many tricks up his sleeve to let that happen.
All in all, it's a landslide for Kotomine and Gilgamesh.