Re: Seidokan Aikido
Well, as far as a practical self defence application *as a beginner*, I would give someone with seidokan a slight edge- simply because our techniques tend to to be simpler in execution, and because because our philosophy is to train realisticly. With enough training both styles likely equally effective, but I think seidokan is a little easier to learn.
I have to agree with everyone else who has said that the teacher and the people should be your primary deciding factor. I would personally recommend Seidokan over Aikikai, as my experience with it has been very good, and I personally prefer it over what experience I've had with Aikikai, but that is only a personal preference. Try out both and see which fits you best.