Hi Brad
I am absolutly addicted to battlestar galactica, I have in actual fact lost count of the amount of times I have watched it front to back. Like you, im sure, I can't wait for the last episodes to be shown to find out all the secrets that ron moore has tortured us with.
I have speculated many of the cast to be the final cylon and I am still not really convinced who it is but my best guess is it's Romo Lampkin (Baltar's attorney) The reason I am more inclined to think it is him is for two obvious reasons. He was cast again near the end of season four in a sort of sub plot with Lee Adama to find the next president. Ok Ron could be just trying to fill the gaps, but I just found it strange that they decided to shoot this plot so I believe it was simply to remind us of Romo. Also, when he told Lee he had picked him as the next president then pulling a gun out on him, this showed a differnt side of his charactor which could indicate he is a cylon. we know him as being very strange but super intelligent and he also knew Grandpa Adama which he said "he taught me everything I know". this could all tie in well with Caprica. He could project images, as we saw with his cat but for me the cherry on top of the cake and the thing that really swayed me towards him was at baltar's trial. When Romo was questioning Tigh, Tigh started to hear the music. Now I know tigh was hearing the music before but there was one sceen where Anders first saw Torrie and their senses to the music they was already hearing seemed to get more intense. I believe this happened to Tigh when he was on the stand. Ans just one last point, Romo wouldn't have been able to follow the music and meet up with the other final five because he is not based on galactica as far as I know, I believe he is based elsewhere on the fleet.
The second thing I have noticed from watching it over and over is the strange use of 'Time travel' Now, as far as we know, they do not have any technology to time travel but this has happened quite blatently twice in the show. the first time is plain to see when Starbuck disappeared for a couple months and only experienced a few hours, arriving back with and brand new Viper. (can't remember what the model is but it was one of the older ones)also,She went back to see her dying mother with Leoben. i believe the Viper was straight off the production line back when they was being mass produced. it was proberbly given to her and planted for her by a cylon manipulator (as you mention) to guide the fleet to earth. The second time that Time travel happens was quite strange because I only noticed it after I had watch it a couple of times. In the forth season not long after roslin and co jumped away on the base-star while adama and all were trying to work out what had happened, a Rafter jumped in. There was no communication from the Rafter so one of the pilots space walked and reported that it was Pike and he was dead. Then I don't know the exact time differance but quite a while later, infact im sure it was in a different episode we saw Pike jump back home to galactica just as he got injured in his rafter. This happened when the cylons and humans were attacking the resurection ship. The point is we saw him arrive at galactica before he had jumped home and it supposed to be shot all in real time. Because of these strange incidents I believe when they jumped into earths orbit, they had actually time traveled into earths future which would explain the nuked planet. This would also give them a route towards actually having an ending where they get to a civilized earth if they can work out the time travel.
Anyway, I hope Ive got you re-thinking about battlestar galactica theory's because I think you are great at it. I really liked your alternative ending, that was great. If you don't already, I really recomend re-watching BSG from the start again. Believe me it is just as entertaining and you spot loads of things you missed before.
Anyway keep it up. great site, love the telephone box! genius!

Take care
Richard Reeve