Justifying sub-optimal research quality by lack of supervision When starting a Ph.D. position, one naturally expects that there should be some kind of supervision of his work. That is, their advisors should be aware of the state-of-the-art and be willing to sit and discuss research directions and provide pointers to the literature. In some cases, advisors may be too "bossy," expecting their students to be "good soldiers" doing what they are told to do without many questions about its research value. However, it's also not uncommon for advisors to be "hands-off," basically  leaving their students on their own and so they come back only when they have something to publish.

Navigating solely through the literature is arguably the worst part of Ph.D Grind. It's all too easy for a student with undeveloped "feel" for problems to spend months trying to shape a proper research plan. That is what happened in my case, where I needed more than a year. Now that I've started with actual experimentation I realized that the workload may be a bit high for a single person. Therefore, I'm expecting that I'll need more than a year before I start publishing results.

Given that I'm working totally independently on my Ph.D. degree, can I state that to future academic employers as a justification for what could be sub-optimal research work? or would that sound like I'm not taking full responsibility?
You should be very, very careful about seeming to criticize your own department or supervisor. It might be unfair that you received sub-optimal results, but if you try to blame somebody else for your results, search committee members are much more likely to just think you are a complainer or a malcontent. 

The best advice at this early stage in your career: either find a way to work together better with your advisor, or switch advisors.