I don't think easier deployment and maintenance is that simple. Each manifest may become smaller, but now you have to maintain multiple small manifests. And keep them in sync. And make sure that they are all compatible. There are pros and cons to any sort of decomposition like this.
With regards to targetting specific components for change, I think what will really solve your problem is having a single CF deployment composed of multiple releases. E.g. uaa as its own separate release within a single CF deployment. If you wanted to, you could update the uaa release itself instead of having to update all the jobs. You still have the problem of, if you only update one component, how you know it's compatible with all the things you don't upgrade, but it sounds like you're already willing to take on that complexity.
This decomposition of cf-release into multiple releases (composed into a single deployment) is currently underway.
With regards to scaling down etcd, I wasn't able to understand the problem you're hitting. Can you provide more details about exactly what you did, in what order?