I take it from what you say that you already have an EPA with you as the attorney? But unfortunately, when that was made you didn't name your son as an "alternate" (that's not the right word, but you know what I mean)? But the EPA hasn't been registered?
It is possible to download the appropriate forms from the guardianship website
http://www.guardianship.gov.uk/ and fill them out without any contact with a solicitor or consultant. This presupposes that you haven't registered an existing EPA.
You probably won't have any problems doing it this way, unless your wife has other heirs that might take exception. That's when it gets sticky, because you are, to a certain extent circumventing the rules. In effect, if you try to register this new EPA, and someone objects, the fact that the consultant has said that she she is not competant will be enough for that EPA to be set aside. Furthermore, you might then not be considered trustworthy enough to administer the existing EPA. Sorry to be so depressing about the whole thing. If you don't do anything, and you die before your wife, your son would need to apply to be a reciever: it's more expensive to do it this way, and more hassle but it is doable. In your situation, I think I'd be inclined to leave things as they are: you could defintiely make things worse.
As for the will - I really don't think you have any choice here. If she makes a new will, and it proves to be invalid I am not certain if the old will comes into force, or if it is as if she had died intestate.
This is all just my personal opinion, but I think that the consultant stating that she doesn't have capacity anymore would be enough to stop me trying to make any changes to the current situation.
Jennifer