I'm gonna jump in here...feel free to shout me down if you like.
The whole 'Size matters not' comment, I feel, has been taken out of context. To me, it is not to imply that the Jedi had unlimited Superman style power but to indicate that someone shouldn't feel it is impossible just because a task or object is bigger than they thought it was. 'The Force is more than this crude matter' (or something like that) indicates that knowledge and is far greater than what we store it in. From that, the power comes from the confidence to use it in the correct manner. Limitation comes from not knowing how to apply that power.
Going off track for a moment, Bruce Lee had pretty much the same quote in different words - 'Having No Way As Way' meaning to limit yourself to one method means you deny the other 9 methods that would get you to the same result (if there were 10, of course!) In this case, Yoda means to show Luke that even though he is a tiny creature, he is able to tap into the Force to move an object far greater and heavier than he is.
Going back to why they just didn't wipe out huge armies with a flick of the wrist - of course it's a plot point, but also consider this: it obviously takes a lot of effort to tap into the Force to do a lot of things. Luke's retrieval of his lightsaber in ESB shows this to be the case, as does Yoda saving Obi-Wan and Anakin in AOTC. The limitation in this regard is to show that whilst the Force is an 'all powerful mystical energy', it is not all encompassing, requiring the user to focus on one thing (or a few things) at one time. Retrieval of Dooku's solar yacht would have meant lessening his focus on the large weight that was bearing down on him - and we're not exactly privvy to whether Dooku was also pressing down with it beyond his hands indicating so, which meant Yoda had to concentrate on saving his fellow Jedi. Also, a case in point is Yoda being unable to fully repel Palpatine's second attack in ROTS. With a dark shadow hanging over the light of the good side, it seems like the Jedi are unable to fully call on their powers - another plot device, of course.
As I said in a previous thread, why didn't old Ben flick his wrist and force push Vader away - we're talking about a Star Wars universe that hadn't been cocked up by George's retrofit of Jedi being martial artists plus factor in that Ben has been in hiding for so many years. Use of his Force skills would have sent a ripple to Vader telling him exactly where he was and thus endangering Luke as well. It's the same with Yoda, but since he's a grand master and Ben only a master, there is obviously some difference in their skills. Vader, obivously, has no human limbs left, so is unable to muster more than a Force choke and a pull in the Force (to retrieve Solo's gun on Cloud City), but even he is only 40% human due to the injuries from Mustafa and the Force only works with living things...
Anyway, if I've misunderstood, sorry. If not, I hope I've put forward enough conjecture for thought...I'm not flicking my wrist to push anything away btw...I'm far too old to use skills like that now!! :p
