I upgraded from a 5D to a 5D mk II, and I thought like you at first, as I was happy with the 5D classic's resolution..
However I'm surprised at how quickly I've got used to the 5D mk II's 21mp resolution - even if the size of the RAW files it creates is a nuisance!

I love taking a portrait with it and being able to zoom into the pores on the subject's skin - the amount of detail there is amazing.
For most applications you'll probably find you don't need the extra resolution. I recently had some prints made for framing, and I ended up having to
reduce the resolution in Photoshop in order to get the print company's preferred DPI! (on the 5D classic I needed to upsample).
However the extra res comes into its own if you want to crop part of a picture, and still have a usuable resolution for enlargements.
Apparently a Kodachrome slide contains around 20mp of picture data, so it could be argued that the 5D mk II, Sony A900 and Nikon D3x are the first SLRs to produce higher quality results than film was capable of - and of course that's before you consider the ability to shoot at high ISOs way beyond ISO 200, which was the fastest Kodachrome emulsion on the market.
I was toying with the idea of running a Nikon D700 alongside the 5D mk II (I still have a couple of Nikon lenses from my film days, including a nice 50mm f/1.2), but that would seem like a step backwards in terms of IQ now.
Id still like to continue shooting with the 5D though, im just worried about a possible noticeable difference between the two purely due to the resolution (even though I am happy with the 5D)
I don't think you'll find a jarring difference in terms of IQ - but what you will notice is the 5D mk II's superior noise handling. I've found that noise only becomes noticeable from around ISO 4000 upwards, whereas on the original 5D I wouldn't want to go higher than around ISO 800 or 1000.
Are there any obvious disadvantages to shooting lower than the max resolution? Ideally id like to get it close to the file size/resolution of my existing 5D.
I can see your logic, but I think it would be a shame to "cripple" the output of the 5D mk II to match your original 5D! Personally I'd be looking to upgrade all my 5D bodies to the mk II
A.