I've tried to follow this thread as best I can but not having a legal mind it turns my brain into porridge, in spite of that I've had a couple of thoughts.
I would have thought that if City are saying the investigation/process is flawed, then they will have to present compelling evidence, but if this is the case then it's probably only City's first line of defence and they will have further hopefully stronger arguments to defend themselves with.
Any evidence based on City's accounts may be sensetive or confidential in nature and so the club would be wise to try and win it's case without having to present it.
The charges seem to only relate to financial matters rather than anything that might have directly affected the outcome of any matches, so to retrospectively void any of our title wins or even deduct points would seem unreasonable and would have difficult to resove cosequences for other clubs.