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've often thought this too. In particular, I've thought that he was enamoured by the sogo bujutsu elements of koryu. It's interesting how time have changed. We now hail a cross-trainer who incorporates unarmed and armed separate systems together and finds underlying similarities as a genius, whereas in earlier sogo bujutsu training this is a given and there is little need to go outside the ryu.