@Mr. Lookforward  or any other fellow advisers here who can advise us on my case which is less or more similar to others but with a bit of tweaks and complex which made me post a new thread here.

- My wife is EEA national from Lithuania  who live in the UK since 2004 so if she try to get British passport based on her country citizenship law she will lose her original citizenship ( EEA citizenship) and so my right to leave in the UK as EEA family member will be ceased , so I guess this is not a good option for us.

- I (none EEA )married her while I was on different type of visa , then I had quit UK and returned on EEA family member joining visa on Feb.2009 , soon after I applied for EEA2 ( Resident card ) and I got it again stamped in my passport in Sep.2009 and valid for five years until Sep.20014 

- Since 2004 to 2009 my wife (EEA national from A8 section European countries including Lithuania) had part time work and self employed works , although she applied for Worker Registration Scheme (WRS) and still has proof of her application but she was not issued registration because she was working under hours and not full time

- Since 2009 that I joined her back here on EEA family member residency , I straight away started working for big corporation with full time ongoing and have full record of my payslips and P60 , most of home bills are on my name and I pay for rent etc. Counsil tax and TV license are on her name and she pays from her bank account.

- in 2009 she got pregnant and took maternity leave from her self-employed work and since then she didn't return back to work until now (2013) , our son born in December 2009 and got British passport.  She has all self-asesstment tax forms and working history including letters from employers in the past on part time jobs.

- For applying on EE4 that I guess I can start after Feb. 2014 we have all documents ready even my life in the UK test that I just passed , except one thing: Worker Registration Scheme (WRS)  which was never completed due to her under hours work between 2004 to 2009 , now this is written in EE4 form HomeOffice guideline :

'' *** From 1 May 2004 until 30 April 2011 

nationals of Czech Republic, Estonia, Hungary,
Latvia, Lithuania, Poland, Slovakia and Slovenia
(known as A8 countries) who wished to exercise
their Treaty rights in the UK as a worker were
required to register their employment under the
Worker Registration Scheme (WRS) for a period
of 12 months unless they were exempt.
If you are applying for a permanent residence
card and your continuous 5-year period of residence in the UK in accordance with the regulations includes a period when your EEA national
family member was required to be registered
on WRS then you must provide evidence of this
as stated in section 11. If you cannot show that
they were registered as required then you will
not be issued a permanent residence card. ''

so based on this fact I might not be able to get EE4 UK Permanent Resident as I understood so I'll become automatically permanent resident even if I don't apply for EEA4 Permanent residency card, right? good, but

Would I be able to apply for naturalization one year later even if my EEA spouse who currently is housewife and doesn't work and was only working part time since 2004 and as result is not able to provide WRS (although she has proof that she applied and sent her documents for registration WRS to HomeOffice in 2005  but was not  issued WRS  because under hours working or other their reasons that we don't know ) 

If so would would be best option in our case case to do ? 

Please advise. Grateful to any good advise , Big thanks.