Good news. I received today my RC!
Brief summary:
I have applied for RC 3 times! Two times the application was returned with a generic letter akin "there is no enough evidence that such and such is exercising treaty rights in the UK".
Apart from the usual documents such as passports and marriage certificate we supplied invoices, checks, bank statements all three times (each time fresh bank statements and invoices). The second and the third time we added self-assessment form. The third time a printout of my husband business website was added.
Right after we sent the application the third time (22 June) we also sent a letter of complaint to the NWC and since the NWC seemed to ignore/forget/misplaced the complaint we sent a letter to the MP. My husband's colleague (British citizen) wrote a letter of support to the MP too saying that he knows my husband who works and pays taxes etc. and that he could not understand why we had been treated in such a way by the UKBA.
Some time later we received a reply from the MP saying that he contacted the office of Teresa May. Soon after that the NWC finally replied and so did the UKBA. They promised to send the COA within 2 weeks and actually sent it 3 days later, that is on September 29.
The RC was received today, on 9 November dated 23 October.
Now, if you have a similar case I would suggest the following course of action, and by "course of action" I don't mean applying for a job at McDonalds.
Send the EEA2 application, some time later request the passport return. Not necessarily but you have a good chance of the caseworker to look at the folder. He even might open it! If the case-worker "does not like" your application or does not even feel like opening it because you know you are self-employed and pain in the gluteus maximus, he/she will return the passport and all the documents accompanied by a useless generic return letter.
Now, ASAP prepare the fresh application and send it to the UKBA, and immediately after that send a letter of complaint to the NWC. Explain that you sent the EEA2 application with all the documents required by the Directive, Regulations 2006, EEA2 guide and their own instructions and received a useless generic return letter from the UKBA.
Wait for 3 weeks during which the NWC have to respond. If they don't respond, write a letter of complaint to your MP. In the letter to the MP complain about the same you have complained in the letter to the NWC and also point out that the NWC ignored your complaint.
Be specific, include all necessary details - the date you sent the application, the date it was returned, the date you sent your letter to the NWC. Keep record of your immigration history events. Five years until the PR is long time to go and you cannot afford forgetting a date or missing a document.