Yes, as long as she has been on FLR(M) for at least 2 years AND has now passed the Life in the UK test, she can apply for ILR at any time between now and April 2014.
In terms of meeting the ILR requirements, the only reason she had to apply for another FLR(M) (I won't call it a Biometric Residence Permit because ILR is issued as a Biometrics Residence Permit as well) was because she hadn't passed the Life in the UK test... so as soon as she passed it, she became eligible for ILR.
Then, once she has received her ILR, she should be able to apply for citizenship immediately, as long as she meets all the other requirements as well.
You were asking if you needed ILR before you could get citizenship... well, now I can see why you were confused, because your wife has been here for 3 years on 2 FLR(M) visas, not the usual 2 years on FLR(M) and 1 year on ILR.
The FLR(M) visa is only valid for 2 years but you cannot qualify for citizenship until you have been in the UK for 3 years... so normally the only way you can legally stay in the UK for those 3 years to qualify for citizenship is to apply for ILR after 2 years, not another FLR(M) visa (the only reason your wife was allowed a second 2-year FLR(M) visa was because she did not qualify for ILR, otherwise she would have had no choice but to apply for ILR in 2012).
This next part doesn't affect your wife at all, but they changed the visa rules in July 2012 and now anyone who applied/applies for their first visa after 9th July 2012 has to spend 5 years on FLR(M) and also apply for ILR, before they can apply for citizenship... so even though citizenship only requires 3 years of residency, because you must hold ILR first, new visa holders now have to wait 5 years to be able to apply for citizenship (and apply for up to 4 visas beforehand - either a fiance visa, two 2-5-year FLR(M) visas and ILR, or a 2.5-year spousal visa, one 2.5-year FLR(M) and ILR)!