I was thinking about writing a lengthy reply, but I think it will only confuse you. So I have decided to write what is the position regarding your wives particular case.
So, to apply British Citizenship when applicant is married to a British Citizen, there are various requirements.
One of the statutory requirements (which your wife does not meet is) that the applicant must be free from "immigration time restrictions" on the date of naturalisation application.
Your wife is living in UK under eea regulations as "family member of eea national" ( ie you are being treated as a EEA national rather than a British citizen because you lived and exercised treaty rights in Spain and your wife was with you).
You wife will only meet this requirement on the 5th anniversary of her arrival in UK. To prove her residence from January 2011, she will have her passport and the arrival stamps on the passport. When she applied for residence card, that application itself is a proof she was here.
Also please keep in mind, she will have to show that she meets Knowledge of language and life requirement.
Right now the requirement to show KoLL is producing two proofs
1. Passing a life in the UK test and produce the letter.
2. Show a B1 Level cefr level qualification in English Speaking and Listening. (various way to show this)
These requirements might change or get amended by the time she applies. Right now, Life in the UK test has no expiry date. So, in all probability, if she passed this test now, it will still be valid at the time of application.
Naturalisation applications are expensive. Right now the fee is £874. So, my humble advice would be to apply on form EEA4 for PR when she is been here 5 years. This application costs £ 55. If she gets confirmation of PR after eea 4 application, then you will know she is has met all residence requirements for naturalisation too. She can then apply for naturalisation with exact same residence proofs that she submitted on EEA4 application.
Please note, to apply for EEA4, there is no KoLL requirements, but for naturalisation there is KoLL requirement.
PS: For other members who are reading this. Please note that the residence requirements and the calculation of dates of possible future applications is based on Nick's wive's particular circumstance. ie SPOUSE OF A BRITISH CITIZEN WHEN THE BRITISH CITIZEN HAS EXERCISED TREATY RIGHTS IN A EEA COUNTRY AND THE SPOUSE IN QUESTION HAS STAYED WITH THE BRITISH CITIZEN IN THE EEA COUNTRY.
For people in other circumstances, the residence calculation may be totally different.
regards