Good one on the observation about the implications behind Luke's comments about the familiarity of Dagobah, OP. Like some of the other posters, this had never occurred to me (and I've spent a lot of time thinking about the Prequel Trilogy that the dialogue of the OT hints at, but which we never got).
Biowings makes some very good points about the ridiculously rushed turn that the Republic makes into the Empire (and about the clear implication that "Clone Wars" refers to more than one conflict). Personally, I think Episode III (I'm referring to the hypothetical one, not the one we got, which I find irredeemable) should have ended with only the very beginnings of the Empire having been established, so that by the time we get to Episodes IV-VI we're shocked by how complete that change has become. Having Episode III end with OT-style Imperial uniforms and Star Destroyers, the Death Star already under construction, and Palpatine already looking like the hooded death-spectre he becomes in ROTJ is just plain stupid. It's an insulting bit of pandering to an audience the director contemptuously assumes is too stupid to understand what has occurred unless everything looks exactly as it does in the OT.
This is just another example of the PT having been made with zero respect for the Saga as an episodic continuing story. Wouldn't it have been great if the PT never explicitly showed that Vader is Luke's father, that Leia is his sister, and that Yoda is actually a tiny green critter? Likewise, imagine if the PT had ended with a Palpatine who, having just declared himself Emperor, still looked more or less like the charismatic Senator he had been at the start of the Saga? Imagine how much more impact it would have to return to him in TESB and ROTJ, and seeing how ultimate power and isolation have turned him into a shrouded, wizened monster...
Lucas won't live forever. Once he's gone, and once the ST and spinoffs are said and done with, I hold out hope that Disney could give us a decent remake of the PT - which they could market as an "alternate" version of the story, so as not to seem disrespectful to GL.