Re: Unifying the theories
In the "traditional" Daito-ryu approach, students start with jujutsu - just the regular ol' Ikkajo-Nikkajo-Sankajo-etc. curriculum. Next, they learn very specific, narrow aspects of IP and aiki, to apply to those jujutsu waza... Aikijujutsu. The "pure" internal training, Aiki-no-Jutsu is introduced last. The environment where I came up was more of a mixed approach, however, with an informal rotation of jujutsu, aikijujutsu and aiki-no-jutsu practice over the course of a season.
I like I Liq Chuan's approach of focusing on first unifying the mental and the physical (developing awareness, learning how to use intent to operate the body; learning the principles and qualities of movement, and unifying the body through them (aiki within oneself). Next, students learn to "unify" with a partner, through a series of hands-on practices that develop connection, sensitivity toward what the other person's body and intent are doing, and the first stages of martial interaction (application of aiki on another body). The jujutsu (qin-na) and freestyle martial engagement come later.
Personally, I find working on the internal development - awareness, intent, unifying within the body - first, is pragmatic, mainly because I have been exploring martial arts for 40 years now, and already have plenty of martial tools. For someone who is entering martial arts for the first time, if he/she is anxious to acquire fighting skills quickly, an internal art with a "unify your body first" approach will not provide what they want. However, someone who wants to build a really solid foundation and is willing to invest the time -- a couple of years, on average -- to lay the basic bricks and mortar, this approach will pay off greatly down the road, IMO.