UKBA application process delayed

I am a Ghanaian and I got married to EEA national in 2003, which resulted in me been issued 5years of stay in UK.
Consequently after the expiration of 5years in the UK, my wife and I submitted application for permanent residency through a lawyer precisely August 2008. The UKBA issued me a letter of acknowledgement advising not to call the agency until 6months. After a year and 7months, they decided our case by sending my wife passport with her permanent residence card. This delayed has caused us a lot of despair because the employer continually demanded for my passport with stay on it. During this waiting period, I occasionally embank on taxi touting which resulted in me been arrested by plain cloth officer, where one of them accused me of assault because he had a bruise on his leg on the cause of arresting me. I was charged to court and the case is still pending.
This resultant effect made the case officer at UKBA to withhold my passport. The letter that accompany my wife’s passport to my lawyer stated ‘’we are unable to decide your above name client case at this time due to intending prosecution. The document submitted with this application has been retained on our record for when we are able to make a decision on this case’’
This has been so frustrating and disheartening to us that after delaying us for 2yrs and caused us emotional distresses, they had to wait for the result of the civil case in court.
Can anyone advice on this issue please. What is the EU legislation on this issue?