I am trying to organize many thousands of photos on my iMac, and finding iPhoto not quite up to the job.
So I started looking at using Aperture. It looks good from the descriptions, but there is a big difference
in the price between the App Store (79.99) and the Apple Store (219.00 - Canada I think).

One user review on the App Store says it is not a full version and hence disappointing, but this is not
mentioned in the description.

Can anyone comment on this ?

Surprisingly not - the version of Aperture sold in the App Store is indeed the same as the version that previously sold for much more. The controversy and criticism is aimed at iPhoto 9, which in the eyes of some, has been "dumbed down" from previous versions. There's a long-ish rant/thread at www.macrumors.com called "iPhoto 9 Sucks" that goes into all the gory details. At the current price, Aperture is a steal, and in combination with Pixelmator, a much better value than Lightroom and Photoshop or Elements.

Hope that answers your concern,

Happy Mac'ing!

Dan