In order to apply for British Citizenship using her EU citizenship your wife has to show a) that she has permanent residence; and b) has been resident her for 12 months since she acquired permanent residence. The right of permanent residence is acquired by EEA citizens by law under the european rules after 5 years residence in accordance with the relevant european regulations. Unfortunately in your wife' s case she needs ot show either that she registered under the Workers Registration Scheme or was exempt. Exemption applied to the self employed and to those already in lawful employment. If she cannot do that then she was not exercising EU rights in accordance with the rule and cannot obtain citizenship by that route. As the wife of an UK citizenship she is eligible to apply after three years lawful residence but she needs to free of immigration restrictions before applying - the full requirements are set out here: http://www.ukba.homeoffice.gov.uk/britishcitizenship/eligibility/naturalisation/spouseorcivilpartnerofcitizen/
The problem is that to be free of restriction as en EU citizen she needs to be here 5 years and to do so as as spouse you have to apply for a spouse visa and then wait 2 years so it is likely to be 2016 before you can apply anyway . Sorry but there it is .