In truth, for the newbie, there is no difference between the United States Aikido Federation and The Universal Soke Council of Enlightened Masters of the Universe.
Well, I have experienced both as a newbie and there was a difference. After 6 months with the soke (Juko-kai) and after 6 months with the USAF school, I could easily figure out who is full of it and who wasn't. 6 months is still pretty newbie status. The soke-dokey talked a lot. They talked a lot about how they were right and everyone else was wrong. The problem as newbie you start to believe what the soke-dokey is saying and then start buying into a system that is simply made up and nothing they profess it to be. They always talked about how great their "lineage" was how "traditional" they were. It was not true. The USAF school just taught aikido and spoke about their aikido, not the aikido of others. Classes were about training not trying to convince the students in the class that we're doing "the right thing."
If I had known what to look for in lineage when I started with Juko-kai then I would have been able to go to the more authentic aikido school that was just down the street from me. The USAF folks thought nothing of you asking about the sensei's background, if you started asking about the soke's background you start getting a lot of hemming an hawing, and he had so many certificates on his wall you couldn't make head or tails of it. Then if you push it you get the standard "well, if you don't think we're effective, then you can challenge, him." b.s.
If lineage is not an issue to you and if you are truly confident in your abilities then you shouldn't have a problem with saying I've trained, here and here, but I haven't train under a formal organization. Tell the truth, don't make excuses for you not having a perfect lineage. If you treat and respond to it as a big deal -- i.e. thesis statements as posts that I only skim, btw-- then the issue is that you have an issue with people asking you about your background. Stand on your own two feet and down't worry about it. Tell it like it is and let it go.