The 100-400 lens is a very good lens and the zoom range gives you a lot of flexibility. When the subject is close and the light is low, the 300mm f4 wins due to the wider aperture.
You can use a 1.4x TC without losing much quality. That will result in 420 f5.6 lens with IS. So you gain a bit of focal length. You can also check this:
Canon 300mm f4 L IS USM or Canon 400mm f5.6 L lens? - Indiawilds: Land of the Tiger. Conservation, Wildlife Photography, Communities
The 400mm f5.6 L USM lens is also a sharp and light weight lens. Good for handholding. However, if it is your only lens, then it would be difficult for you to click large mammals like elephants when they are close. Also the widest aperture is f5.6 like the 100-400mm lens.
I use a dry box to control the humidity, so that there is no scope for fungus. Since you are starting new, I don't expect you to invest in a drybox. You can just get a large airtight container and keep some silica gel in it and keep your lens when it is not in use. I have filmed using the 100-400 in rain and haven't faced any issues.
One other lens to be looked at is the 70-200 f2.8 L IS II USM with a 2xIII TC. This combination would be more expensive than all the previous combinations. You will gain the extra zoom range at the lower end.
As far as upgradation of the lenses are concerned, Canon will upgrade the lenses. However, they haven't announced when they will do it. There have been supply constraints as well as capacity constraints due to Tsunami in Japan and floods in Thailand etc. So Canon will decide whenever it is right for them to launch these lenses.
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