Apple has too many things on their plate. The Mac Pro isn't special. You have the iPad Pro (where iOS got very few changes to take advantage of the hardware), the iMac (not Skylake, no TB3), the Macbook Pro (not Skylake, no TB3), Apple Watch (very few updates, app ecosystem is dying), or iOS (getting generally more buggy, UI issues.)
The Mac Pro isn't unique in this situation.
This discussion again, the "Apple has too many things on their plate" has been the most repeated sentence (in different iterations) since the iPod was first released...
Let me paraphrase:
2002 and 2003: iPod with windows-support and later USB was released: Apple doesn't care about Mac users anymore, Windows users will get all the attention!!!
2005: Mac Mini released, "OMG, Why do apple release a toy machine! It's useless, APPLE DOESN'T CARE ABOUT THE PROS ANYMORE, GIVE US 3GHZ G5 OMFG WTF APPLE!"
2007: iPhone relased: "WTF? iPhone OS (it wasn't called IOS then) will take all the attention from OS X, OS X is DOOMED! Apple doesn't care about it's computers anymore!"
2010: iPad released: "See, all the development goes into IOS-devices!!! Why do we need a bigger IOS-device, give us better computers!!!"
And so on... During this time we also got a more or less flawless transition to intel (including the phenomenal Rosetta system), a fantastic development in features, functionality and performance of OS X, a few fantastic hardware and software products (MB Pro Retina to name one) and so on.
Seriously, Apple has like a hundred thousand employees, if you think like 12 different main products with 2 main OS-branches (OS X, IOS incl. Apple TV and Watch OS) is too much for such a huge company, think again... (MB, MB Pro, MB Pro Retina, MB Air, MP, iMac, iMac Retina, Mac Mini, iPhone, Ipad, iPod Touch, Apple TV, Apple Watch). That's like 5 different product categories... (Watch, AppleTV, Desktop, Laptop, Tablet).
Or are you one of those that still think Apple has like a thousand employees and everyone is a part of every product?
Some people seriously seem to think so.
And furter: TB3, was really first released in any way in september and first products with it just started to show, Skylake: Was announced in August and all products aren't released yet afaik.
iMac Retina with the i7 is skylake, so why do you state the iMac is not? the Retina is the top-of-the-line iMac, and the only one really worthy and in need of skylake. Macbook Pro Retina was updated in spring of 2015 and at that time Skylake wasn't released.
What do you want them to do, go away from their age old release schedule to satisfy a few select users need to always be bleeding-edge? Should they center their release date around Intels release schedule instead of when the product is ready?
Of course not, they'll release the products when they think they are ready, and probably a MB Pro Retina w. skylake is in the works and wasn't finished (and/or the previous model hadn't ran its course yet) when intel released skylake...