What are the miles on each? Do you know how well they've been maintained? Yes, you want good shocks but remember, you can always put rebuildables on them (if they don't already have them).
I can only speak for the SDI, as that's what I have. As far as fuel economy goes, I get between 16-20 mpg depending on how I'm riding (closer to 16 if with the fellas, closer to 20 if with the wife). As far as reliability goes....mine is an '05 with just over 9000 miles on it. The only thing I've done engine-wise is to add Boyesen Rage Cages to replace delaminating throttle body boots. Compression is still 145-150. Other than that, routine maintenance only.
It seems to me from reading many a thread on DooTalk that SDI is the way to go if you want "plug and play". If you like to do a lot of mods and want "tuneability", you may be better off with carbs.
You probably can't go wrong with either one. Both great engines!