Pro's & con's of starting with F1:
Pro: 9 generations total, & it's stable.
Con: You might need to grow out a zillion F2's to find what you're looking for, since you just added all the new variables of a third variety.
Pro's & con's of starting later:
Pro: You have got that first cross to give you what you wanted for a few generations already, got rid of the unwanted stuff from those two parents before introducing a third. Much less confusing and need fewer plants in each generation to find the variables you want from the third parent.
Con: Your crossing with a third parent makes the offspring F1's again, so it's eight more generations on top of what you already did.
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