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The goal here is to increase the fluffiness of any army with Allies by adding special rules/requirements to allies that could be taken. It's incomplete, but essentially every army gets two rules: When they are being allied to, and when they are allies. All Battle Brothers armies ignore these special rules.
So, for example, Orks:
As Allies: Orks only work when there's 'Sumfin good in for da boyz.' To represent the allies paying off the Ork Horde to come help, for every hundred points spent you must deduct an additional five points from your list. Alternatively, you can spend fifteen points per hundred and count the Orks as one level higher on the Allies Matrix. (Note that come the Apocalypse armies can never be allied, no matter how many points you spend.)
When allying: When bringing in allies, Orks have to respect the people fighting alongside them. Therefore, one model in their Allies must be designated the 'Umie Boss.' He must be an HQ choice with at least one purchased piece of Close Combat wargear and must have a points value equal to 1/2 or greater the points cost of the Warboss. (If the model is part of a squad or retinue, do not count the retinue's cost when calculating this. You can't become tougher by surrounding yourself with minions!) The Warlord must always be chosen from the Ork formation.

So do you think this is a workable idea? I don't know all the armies well enough to include fluffy allies rules for them, but I feel like this helps with the fluffiness somewhat while keeping things balanced. (The one thing I was unsure on was spending extra points to increase army Synergy. Too much? I can remove that.)
Other ideas include Tyranid Genestealer Cults, (Essentially, they can take a very small number of Allies, possibly even just Guard, but the allies cannot take unique characters, must forgo taking an HQ, and cannot take vehicles except dedicated transports.)