The 70-200mm f/2.8 is will probably heavier with a TC stacked on. With a 1.4X TC, the quality might still match or even beat the 100-400mm lens, but the range is nowhere near as far.
With a 2X TC stacked on, there is said to be a distinct loss of image quality and in a matchup between the two setups, the 100-400mm is a clear winner.
In the end, it might boil down to what sort of subjects you wish to shoot. For example, if you wish to do some indoor sports photographs, it might be pushing it with the 100-400mm, but with the 70-200mm f/2.8, even with a 1.4X TC on, it might still be manageable. That said, someone at this forum did do indoor sports with the 100-400mm before, at ISO 3200 and using a noise-removal software after which.
If you use a 1.4X TC on your 70-200mm, it might still be a little short if you want to get involved in photographing smaller wildlife or birds. For bigger animals in the zoo, it might do well even on it's own, but over here I've found that the more dangerous animals are generally further away and you won't be able to get up close at 200mm, even on a 1.6X FOV crop camera.
And of course, if you wish to shoot primarily handheld, then IS is a good idea. I found myself wanting more range, plus wanting IS because I don't use a tripod. So the 100-400mm was the answer for me.
There's other nice choices out there for birds and wildlife too, such as the Sigma 50-500mm and Canon 400mm f/5.6L. But if you're looking to do some unusual landscape shots and photograph tame animals, then the 70-200mm (IS or non-IS) might be a better choice for you. But quite frankly, I haven't found the focal length range between 55mm and 100mm (between the kit lens and the 100-400mm lens) to be very crucial as of yet, especially since I don't do portrait shots.