C3PX put it really nicely- nobody wants 3PO and Anakin/Padme take him along with R2 to Geonosis. Kind of fits with his "lot in life". Then, R2 and 3PO argue, and what happens is that the headstrong R2 goes in to try to help Anakin and Padme, while 3PO stays on the ship and misses out on all of the fun.
I think this fits better with the original SW. You' remember 3PO's attitude when R2 wants to go a particular way on Tatooine.
"No! I'm not going that way." "You'll be malfunctioning in a day, you near-sighted scrap pile!"
So likewise, in SOTDS, he avoids the danger and doesn't follow R2 (why would he, anyway? They just met. He has no attachment for the droid).
-----------
Lately there was some concern that the 3PO scenes wouldn't work (they felt too "constructed"), but I recently nailed the pacing through a simple dialogue reversal and the removal of a line, and now I'm sure that this is definitely how it will be. No 3PO in Episode I.
And that IS an interesting backstory, but at least at this point I see no way to have it happen both ways....
TM