Yeah, Swampert gets ruined way too easily... and I've even run into a few HP Grass Jolteons and such. Swampert was really only useful for the immunity to Electric-type moves, most notably Thunder Wave - though I suppose Shaymin can sponge those as well.
Yea, I think Swampert could be replaced for Gyrados. Since you mention it's usually fodder, might as well make use of the slot right? Celebi and Breeloom will have a lot harder time switching in on your team as a whole. The only problem is your going to run into a few problems as far as an electric weakness. Until testing says otherwise, I am guessing Shaymin will have to be your Jolteon check (along with Scarftran).