For all those who keep in touch with advancements in field of biology iPSCs ought not to be a foreign term. iPSCs are now being used to make organ models to be able to study diseases and how drugs will affect them without needing any living host. I expect this organ modelling to become more and more advanced in future and soon all complete organs to be made using this technology. However should making a complete living brain ever be allowed for studying diseases as we are mostly our brain, so maybe while using such living brains we are making conscious systems on which we are experimenting?
I agree that iPSCs will continue to be developed and will probably be used to make brains at some point in the future. Whilst it's obviously not possible right now, feasibility isn't the issue here. A lot of my answer will be somewhat opinion based as a result of the nature of such an ethical question.
As to the ethics of experimenting on such living brains, It's undeniably a tricky question - and, as with all ethical dilemmas, suffers from the inherent variability of ethics and morals (you will struggle to find two people with exactly identical ideas about right and wrong, and from a purely logical and scientific perspective there's no reason to believe that moral objectives exist at all).
An interesting phrase that you use in your question is "we are mostly our brain". I suppose it depends on what characteristics you're looking at: a brain alone would be incapable of surviving and by mass the brain only accounts for around 2% of the human body. we are mostly water; simple, lifeless and unconscious.
Therefore we are evidently ranging into territory of consciousness, and by "we" you are referring to our seemingly conscious 'mind' as conjured by the complexities of the brain. As for this, I think perhaps the philosophy stack exchange is the place to go...
Ultimately it depends on whether we look at a brain as simply a collection of atoms which form molecules, cells, tissues and then organs or as something more - this is the whole idea of emergence (for example, an individual ant is unconscious and negligible, but many thousands of ants communicating using chemicals and simple commands forms a highly complex and adaptable ant colony - the ant colony is greater than the sum of its parts). if the former is true, then there should be no difference in manufacturing a brain and experimenting on it to making muscle tissue and performing experiments on that (or even creating a crystal from chemicals and using that for experiments). If we look at the brain as something greater than the simple sum of its parts - as a living, conscious being - then I suppose we'd need to go through the proper channels that we have now when dealing with something that's alive.
From here an infinite variety of problems crop up: would the brain be given the full rights of a human, or treated more like animal test subjects? Would consent from the brain be required? Could a brain even be conscious if unattached to the rest of a body? Would killing the brain be murder as it would be with a human?
So far I've just been stating issues: my personal opinion is that we ought to find a balance somewhere between treating the potentially conscious brain as merely an impressively complex collection of lifeless components and giving it the full rights of a human being. where that line should be drawn? I don't really know. Personally, I'd rather test drugs and treatments on a mere brain than on a fully formed and functional human being, but someone else might not agree.
These questions are always difficult, and science can't really give any reasonable answers (scientists can't even agree on what makes something alive, let alone conscious). there is an entire field called bioethics devoted to things like this. my advice would be to ask this on the philosophy stack exchange as you will get some interesting answers there.