One reason I use the Waterloo line to London instead of Paddington is that the train seats are much more comfortable. When the new stock arrives do you think this will still be the case...?
Well that depends on where your going as to what stock you will get.
That would Exeter to London
Well in that case comfort shouldn't change as you will not be receiving any new or different stock. The only reason it may is if SWR decide to replace the seating as part of the refurbishment, however I have not heard any plans for them to do so.
By the way, Exeter-Paddington will be recieving new hitachi trains in the next few years, and the seating on them is firm and less comfortable. So, if I were you, I'd stick to using the waterloo line, even if it is a little longer.