Hi Glenn, hope you enjoyed the trip!
On the lens limitation issue, I am not sure about this. I think you have in your mind the DxO 'perceptive megapixel' concept which suggests that the lens is only allowing a percentage of the overall 'theoretical' resolution to be realised, in effect turning the 24 megapixels into (if memory serves correctly) about half that in real life. I find this concept quite confusing. While I understand what they are trying to achieve (given the problems and complexities of understanding MTF numbers) it is also evident that the perceptive megapixel measurement changes depending on which body the lens is attached to. It attempts to measure the resolution of the overall package rather than the lens itself. This suggests that having a greater sensor resolution (ie megapixel count) would result in a different and probably higher perceptive megapixel reading. That said, as I have noted, the 90D is only has about 15 percent more pixels horizontally and vertically, so the overall resolution gain is not spectacular. I don't think that having the extra resolution is a bad thing, particularly given that tests seem to suggest that high ISO rating (at least up to about 1600) is no worse than the 80D. Whether this is worth the outlay for the 90D, though, is the question given that other upgrades seem mainly in the live view experience.
I think there are two distinct (but related) issues with through-the-viewfinder focusing. The first is the focus hunting issue. As you know this is inherent in the DsLR phase detection focus method, as the focus sensor struggles in low light and in low contrast situations. Your comments suggest that it is no better in higher end models than in the 80D. This is very old technology now and perhaps we are at a limit where the cost benefit ratio is simply not worth the redesign of the sensors to increase the sensitivity, given the decision to put resources into mirrorless. The light sensitivity of phase detection focus also means that the number of focus points available is reduced as the aperture gets smaller, and this focus method often does not work well at apertures smaller than f/8. At 400mm, the 100-400 is at f/5.6 which is about as low as you want to go and still get reasonably good reliable focus in low light. I have found the 80D to be fine in straightforward situations with well defined edges and contrast - fast and accurate - so its not a huge problem, but from time to time as you note, it gets completely fooled. Clearly (and perhaps reassuringly) its not unique in this. Likewise, I think that the contrast detection system in mirrorless also struggles in 'uncontrasty' situations, as this uses the point of highest local contrast as the focus point. But there does seem to be steady improvement in both focus speed and sensitivity of mirrorless as companies develop their on-sensor systems, to the point that I expect that on-sensor will be preferable in terms of both speed and accuracy (we are perhaps already at that point).
The second issue is focus tracking - ie the ability of the focus system to follow a moving object. The 80D (and the 90D) seem to have problems both with the ability of the focus to 'hang on' as the subject moves, and the ability to intelligently track the chosen object - when viewfinder focus is used. I expect the 5D series (and the 7D2) are better in this regard, but have never used them. In this area, the live view experience is very good (if ultimately not quite as good as Sony's most recent iterations) particularly in terms of 'colour tracking' for things like face and eye detection. I've tried this in live view on the 80D and it seems to work pretty well, and by all accounts the 90D is better. In contrast, I find the viewfinder experience to be pretty hopeless with the focus points easily confused by background. Its better for birds against the sky where the bird is the only 'hard' object in the frame.
You must have done a lot of BIF on your pelagic - how did you find it?
I may well end up getting the 90D because I want to have a second body as a back stop when travelling (which would then be my current 80D). However I will wait and see how prices go in the lead up to Black Friday, Christmas deals etc. The M6 Mk2 looks surprisingly competent (and apparently works well with EF lenses with Canon's adaptor) but I don't like optical viewfinders.
Simon