Is this regular and consistent with the immigration rules?

[beminegh]

I applied for an Indefinite Leave to Remain (ILR) on 6/5/2014 and received my refusal decision on 19/5/2014 against Paragraph 287 of the Immigration Rules (a) (ii) and (iii) which state:
(ii) The applicant is still the spouse or civil partner of the person he or she was admitted an extension of stay to join and the marriage is still subsisting.
(iii) Each of the parties intends to live permanently with the other as his or her spouse or civil partner.

I quickly responded by making an Application for RECONSIDERATION on 20/5/2012 and argued that the decision was incorrect and submitted all the necessary documentations to proof otherwise of the above and requested the decision to be overturned. Then on 25/5/2014, I received a bio-metric having been granted another 2 years Leave to Remain (LR) with an explanation note that:-

“It is accepted that you ARE YOU in a genuine relationship. However, you do not meet the requirement of the Immigration Rules whilst you continue to live apart as this casts doubts on whether the relationship will continue to subsist''. Then

Unfortunately, there is not a single immigration rule or provision that is supported by this argument. Very strikingly, the UK Supreme Court’s judgement in Alvi, given on 18 July 2012, established the following:
‘Any requirement which, if not satisfied by the migrant, will lead to an application for leave to enter or remain being refused is a rule within the meaning of Section 3(2) [of the 1971 Immigration Act]’. This means any requirements must be agreed by Parliament, the precise details needing to be put into the Immigration Rules. After the Alvi judgement. Therefore, it is unlawful to refuse an application on the basis of requirements not included within the Immigration Rules.

It is explicitly clear on the qualification for ILR as a spouse and the regulations is that to show INTENT’ to live together. It is NEVER stated that a refusal is justified because partner and you temporally live apart. For emphasis this is what the regualations says
''intention to live permanently with the other’ or ‘intend to live permanently’ means an intention to live together, evidenced by a clear commitment from both parties that they will live together permanently in the UK immediately following the outcome of the application in question or as soon as circumstances permit thereafter''.

As the Home Office is been intransigent by approbating and reprobating on issuing me with ILR, what should be my next line of action? I have considered writing back to the Home Office (Cardiff PEO) drawing their attention of the illegality by misinterpreting the immigration rule and ask that I will proceed to Judicial Review if they do not change their decision. But before doing all these, I want to know if these are the right steps in this circumstances considering that this case has already gone pass the reconsideration stage.
Thank you for your advance advice