Hey Chris,
Firstly, I want to say that I personally feel that Takeda Sensei was a singularly gifted martial artist, on a huge number of levels. Secondly, it's very obvious that he had quite a bit of training in a few things, so I don't feel that Daito Ryu was just created out of scratch. I feel that there is a very solid basis to the art, and it's one that I'm quite fond of, really.
When it comes to Sokaku's training, what is unquestioned is that he was trained in Ono-ha Itto Ryu Kenjutsu, and probably/possibly Hozoin Ryu Sojutsu. His family background included members who were known to be skilled with such weapons on both sides, and things like the Itto Ryu are uncontested from everything I've seen. Additionally, he is said to have travelled quite a bit, visiting and training at a number of dojo (there are claims of Jikishinkage Ryu, but they are unverified). Then we have his early training under his father, who was, amongst other things, ranked as a Sumotori at one time.
So I'm not in any doubt about Takeda's training being serious and in-depth, what I question is the idea that Daito Ryu itself, an extensive, unarmoured unarmed-heavy system, dates from when it is claimed to (the late 12th Century, stemming from Minamoto Yoshitsune, who is pretty much a romantic hero for Japanese martial arts). Systems like that are really the product of peacetime, and the late 12th Century was the time of the Genpei Wars (of which the Minamoto clan was a large part), which was followed by the Ashikaga period (fairly turbulent), which moved into the Sengoku Jidai (period of warring states), before getting to the Edo period from the beginning of the 17th Century as the first real time of extended peace. Arts predating this time tend to be weaponry dominant, and although they may have some unarmed, it would tend to be less "developed" in most cases. They would also have far smaller curriculums, not the literally thousands of techniques that Daito Ryu claims.
When we look at the structure of what a Ryu is as well, we get some things that are different from Ryu to Ryu, but some things that are fairly consistent. And one of those consistencies is that the art (Ryu) is passed down in a systematised form, allowing the art to be reliably transmitted. When we then turn back to Daito Ryu, Takeda himself didn't teach Daito Ryu as a systematised art, the formalisation and structure was introduced largely by his son, who also reduced a lot of the weaponry work (giving Ono-ha Itto Ryu it's emphasis again). So that's another gap in the idea that Daito Ryu itself has the history claimed.
My feeling is that Takeda was taught a range of things from his father, which may have included a degree of unarmed concepts and principles, as well as studying Ono-ha Itto Ryu when he was young. From there he travelled around, and was exposed to a great number of other arts. With his natural talent and understanding (he was said to be able to watch a technique once, and immediately understand it almost completely), combined with the varied experiences he had, Takeda began teaching what he had learnt, and what he had developed out of it. Later it was given the name Daito Ryu. The biggest influences, though, appear to be the swordsmanship training, which also explains the emphasis in Aikido, as the footwork is very similar to swordsmanship, and the dominant striking attack resembles a sword attack to a great degree. I also feel that exposure to a range of other arts in the area contributed, such as branches of Asayama Ichiden Ryu Taijutsu, which is from the same area, and shares a number of similarities with Daito Ryu, particularly at the early levels (a high emphasis on te-hodoki, for instance, and similar reiho, as well as dealing primarily with grabbing attacks to the arms/wrists). Daito Ryu is more circular, and has a different "entering" feel, but the similarities are certainly there.
Hope that made some sense.
or countries.) 
but I thought I had read that Daito Ryu claims to go back even further than that (A.D. 900, perhaps?).
