I'm up to 6 of these.  Not sure how much more I'm going to army build with this trooper though.  That might have more to do with just how scarce it's been at retail, though.

But I've definitely started to notice the stark differences in the Kashyyyk Trooper's uni and the Biker Scout that was repainted for this figure.  At first I thought that the helmet was the biggest difference.  But it also turns out that the boots are radically different as well.  In fact, the 41st Elite Trooper has the same boots as the Galactic Marine.  The other differences in the uni are negligible, but those really stand out.  Hopefully there is enough talk about this on the various message boards that Hasbro will take notice and make a proper 41st Elite Trooper in the next year or two.  Certainly there is a market for it as this version is selling well even as some of the other Clone Troopers have started to pegwarm a bit.

I was kind of surprised to find a Stormtrooper mini-hologram packed in with R4-M6.  I would have thought that Mace's droid would come with a hero mini-hologram.

The listing seems a little sketchy even though the guy has decent feedback.  I would email him and ask for the following:  The serial number and/or a photo of the base.  Also to see if the original packaging is included.

There have been cases of people painting the chrome Vader's to look like the original edition Vader.  So be cautious, because this piece will routinely sell for over $250.

***EDIT - I hadn't seen the replies immediately above mine.  Plus, look at the chest plate and compare it to the RS image that you linked to.  You'll notice that the controls on the chest plate aren't painted well, and there are some slight paint inconsistencies there.

If it's a window box then it's definitely the ROTS version.

It's best not to wade into the fray that are the RS forums.  I said my piece there and that's that.  Is it going to be tough to get all of these exclusives this year?  Probably.  But I think that GG is providing at least two other avenues to get the Clone Commanders besides going to the shows.  It looks like you should be able to get them individually online after each con and then there's the box set that will be available in the fall.  People seem to keep on glossing over those details.

And the fact that it's a Star Wars Shop exclusive could be VERY significant in the long run.  The last SWS exclusive Clone Wars animated maquette was the Snowbunny Padme which has just exploded in price on the secondary market.

Playing catchup is definitely going to be expensive.  These pieces alone will run you a pretty penny:

1st edition Yoda
1st edition Darth Vader
1st edition Jango Fett
Boba Fett
Blackhole Stormtrooper
AOTC Clone Troopers (the red and blue being the most elusive)

However GG has been going back and revisiting a number of these characters and the second editions have been more plentiful.  Witness the 2nd editions of Yoda and Vader.  They made huge runs on those and they wound up clearancing out for as low as $20.  So if you don't feel the need to be a completist and just want one of every character you might do a little better.  Besides, some of the second edition pieces (like the new Jango Fett compared with the first one) are superior to the first runs.

Aside from eBay there are some options for catching up.  There probably are a number of older pieces that you can still get from some online dealers.  Try doing a Froogle search and you may just come up with some things that aren't widely available.  Conventions are an option, but you have to go there with cash and you need to be prepared to haggle.  So know your market prices.  As for those market prices, they are definitely set on eBay.  The key to buying mini-busts on eBay is tracking as many items at once as possible.  And avoid auctions that close on a weekend.  There's a weird trend going there, but apparently auctions that close on weekends tend to close higher.  Backtracking is definitely possible.  I backtracked almost every piece from the Biker Scout back to the beginning (I already had the blue Clone because I stepped in **** and got lucky at Wizard World Chicago) and to this date I'm only missing two mini-busts and the holiday edition gift busts.  But you're starting off a couple of years down the road and it's going to make this a little more difficult.

As for current items, I tend to recommend the route that I use.  I've got a good relationship going with a local comic shop.  I pre-order all of the general release mini-busts through them and I get a 20% discount off every order.  So a $50 mini-bust winds up costing me $40 with no shipping costs.  You'll just need to keep up on what's up for pre-order through Diamond Previews which comes out at the begining of each month.

As for exclusives there are a couple of options.  First, you can go to the show.  Can't go to the show?  Hook up with someone who can help you out.  Typically those deals involve trading but some people will do cash plus shipping deals.  Then there's the online offerings from Gentle Giant post convention.  They'll usually do that within a week after a show.  Those can go pretty fast, but it is an option.  It'll definitely cost you less than eBay.

Damn though, have you opened up a can of worms for yourself.

TRU's have been pretty bone dry around here as well.  This whole BOGO deal seems like a way to get TSC stock out of the way in time for the 30AC line more than anything else.