Okay, help me with this math:
$8 per fig - Basic Fig
$4 per fig - Clone Wars 5 Fig BP
We know profit margins on these items are high - Hasbro makes a profit on what they sell to retail and retail makes a profit off of us. Lets be conservative at 60% markup for Retailers and 66%. That means Hasbro's cost structure per figure is as follows:
Basic Figs: $8 Retail $5 Selling Price $3 Hasbro Cost
BP Figs: $5 Retail $3.13 Selling Price $1.87 Hasbro Cost
Its not like the BP packaging is free, so let's assume the figure itself costs $1. That would mean basic figure packaging costs $2 and the BP packaging costs $.87 per figure for a total of $3.48.
Your numbers are a smidge off, I'm not at liberty to disclose exact numbers but from what I've seen at places that are NOT my employer, I can tell you the wholesale prices of a Hasbro figure are actually higher than that. And there's also issues of landed costs, which vary from chain to chain depending on what gets delivered where, distribution systems, etc. It isn't free to ship a figure from the Toys "R" Us warehouse to a store, for example.
There are a bunch of other factors that can change the price as well-- and yes, a lot of the time, it's the whims of the store. If they want it to be a loss leader, they can lower their price to increase foot traffic. (It makes sense for Wal-Mart to charge less for SW if it causes kids and collectors to come in and also buy toilet paper. And yes, they have analysis software to determine such things.) With Toys "R" Us, it's not like Target where they can take a hit on toys because they're going to make it up on light bulbs, sodas, diapers, and other goods you could just as soon have bought elsewhere. Toys "R" Us (and stores that are a bit more specialized) really do benefit from the extra $1, or $5, you pay for on some items.
"Cost of prodcut" is very hard to nail down-- in my experience it's not $X for the package and $Y for the figure, but it tends to be a quote on the entire "thing"-- the packaged figure. If it sounds like I'm talking crazy, that means I'm explaining it more or less correctly.
This would follow Adam's logic that packaging adds quite a bit to the cost, but additional figures would only cost $1. Certainly doesn't seem like rational to raise the retail price an additional $5 for adding one figure. 
Of course, TRU raises their prices by $5 for no reason at all... 
Toys "R" Us has very good reasons-- as does Target. They have a business to run, goals to meet, employees to pay, and a marketplace where kids grow up earlier every year. Wal-Mart has screamingly efficient delivery systems (or so I am told), and I've heard very little about Toys "R" Us-- but from peeking in their systems, it doesn't exactly seem to be supremely advanced (again, from what little I gather, someone can probably provide better light on this than I can.)
KB has charged more for years, and Toys "R" Us-- who is also struggling-- will need to do so as well. (Target's $7.99 Joes just seems to be a grab for the extra buck because the product is so hot they have no reason NOT to do it.) It really isn't as simple as one figure adding $5 to the price, but lots of creeping factors causing the entire packaged product's cost to go up-- paint, transportation, prototyping, salaries, all that junk. (It also wouldn't surprise me if the Target packs were nailed down before Hasbro decided they had to do the adjustments in pricing vs. product.)
Another fun example-- DC Infinite Heroes from Mattel. 1 individual figure is $4.99 at Target or $7.99 at Toys "R" Us. (There's a gap.) The 3-pack boxed set? $9.99 at Target. Unless this is some sort of mistake, it really does prove that you can apparently save a bundle by selling figures IN a bundle.
As depressing as it is, we're probably not all that far off from a $9.99 basic figure. It'd probably make a lot more sense (in a "let's keep costs down" way) for Hasbro to do more in the way of Battle Packs and Comic Packs, but that individually carded figure is such a popular format that we'll probably never see that happen. Personally, I'd like to see more sensible (read: not with a figure I already bought) multi-packs just to keep packaging manufacturing down, to reduce transportation costs, and to get me more figures at once. I think the Joe 2-packs of the 2000s were a step in the right direction, *except* for all the repacks and the lack of putting troops in 2-packs for those who were so inclined. I bet a lot of money could be saved and made if the 3 3/4-inch industry focused solely on boxed sets.
