[SalesForce] How to set a default value on lightning component force:inputField which is a lookup

This is a bug inside the framework where dynamically created components are not getting properly indexed to their parents. Doesn't look like anyone is actively working on it right now. If you'd like to put some pressure on the devs who own this you can file a case and tell them to link the case to internal bug W-2529066.

Setting the options doesn't actually cause the rendering to happen. So, the value you're setting is ignored because it isn't valid at the time. The solution is to use another callback post-rendering. Here's an example app I wrote that demonstrates this:

<aura:application extends="force:slds" controller="LightningAccountController">
    <aura:attribute name="accounts" type="Account[]" />
    <aura:handler name="init" value="{!this}" action="{!c.doInit}" />

    <lightning:select label="Choose 1" name="a_opt" aura:id="a_opt" onchange="{!c.change}">
        <aura:iteration items="{!v.accounts}" var="account">
            <option value="{!account.Id}">{!account.Name}</option>
        </aura:iteration>
    </lightning:select>
</aura:application>

// Controller
({
    doInit: function(component, event, helper) {
        // Request from server
        var action = component.get("c.getAccountList");
        action.setCallback(this, function(result){
            var accounts = result.getReturnValue();
            console.log(accounts);
            component.set("v.accounts", accounts);
            // Let DOM state catch up.
            window.setTimeout(
                $A.getCallback( function() {
                    // Now set our preferred value
                    component.find("a_opt").set("v.value", accounts[4].Id);
                }));
        });
        $A.enqueueAction(action);
    }
})

// Apex class
global class LightningAccountController {
    @AuraEnabled global static Account[] getAccountList() {
        return [SELECT Name FROM Account LIMIT 10];
    }
}