Some good responses. Thanks.
One of the main reason's I got interested in looking at Koryu. Is because they informed me of a different kind of martial arts context. As Cliff Judge said-"because the environment that informed koryu is gone".
While it's clear that Aikido is not a koryu, Ueshiba created a system that was so influenced by Koryu, that I think it's almost impossible to understand technical Aikido with out spending some real time trying to understand the techniques of many Koryu systems. Jujutsu systems have the most in common with Aikido, but many of the Koryu I've looked at, share much "flavor" with Aikido.
I think when we study something, at first we use comparison to do that. So when many people first start Aikido, that want to compare it to something they may already know more about. Something like Boxing, wrestling, Karate, Kendo or Judo, is probably something most of us were more familiar with when we started training Aikido. I think this comparative influence shades much of what we think Aikido is.
I find systems like Boxing, wrestling, Karate, Kendo and Judo less like Aikido, then many of the Koryu I've looked at (only from outside study though). This is a very interesting thing to me.
Aikido was most heavily influenced by Daito Ryu, which was and is not a koryu. O'Sensei was able to observe some Koryu practices (historical accounts point to a very limited exposure). It is highly likely that he was not exposed to a lot of the hidden teachings that simply are not shown to outsiders. In that context, making comparisons from "uneducated eyes" can be very misleading. I think that we are best off leaving comparisons to be done AFTER we have gained a fairly substantial body of knowledge in the areas that we are looking to compare. I see this problem surface in the "IP Wars" (my term for the petty bickering that goes on). What we think we see and know, truly is lacking and misleads us.
I do think that people who study Aikido and engaged in formal Koryu training have a variety of opinions as to the overlap and lack thereof. Many of them will not talk about this because of their oaths to secrecy in studying a koryu. I think that trying to get good at any one art (let alone a couple of them- as some of us are apt to try and do) is quite a life-time of accomplishments. Looking back over my years of training, I recognize that many of my previously held beliefs and comparisons, I no longer agree with and am more likely to be quiet and simply to and learn what I can about whatever I am doing.
Happy New Years!