One shot with three dice with TL and focus and a second shot naked

or

One shot with TL and one shot with focus.

Are you shooting at someone with a lot of agility or not? If they have a lot of agility then I would say the one greatly modified result is better because you have a greater chance at connecting. For anything else I'd say modifying the two separate attacks is better.

Expected damage is greater in all cases with the two modified shots vs. 1 TL+F and 1 naked. At least on paper. With that said, instances where it's your only shot against a fat Han, 2 damage isn't going to do anything, so you're going to be better off stacking and hoping for 1 damage every other turn, and maybe get lucky and not need to spend that TL. Or if you think you're going to be closing to R1 (or out of R3), then the change in dice can affect which is better.

But straight up 3 attack vs. X agility, 1 Focus and 1 TL shot is better than 1 TL+F and 1 Naked.

If you've spent your TL and came up with multiple eyeballs you are probably better off spending the Focus token and taking the unmodified second shot instead of saving the token in case you roll some eyeballs.

It's going to depend on what that first attack looks like.

As previously mentioned two modified attacks will, on average, give better result BUT you aren't rolling both attacks at the same time so you get to see what happens with the first attack before deciding how to spend tokens. There may be a 'right' answer to this when averaged across all possible attacks but when it happens in the game you are going to have a lot more information to work with.