It won't be a waste, since many thins are similar (everything you'll find in 3.5 is also in 4.0), but why go for an older version? I've got my MCDP 2005 (.net 2.0) and it is still relevant today (although I don't have an official certificate for any of the
3.5 technologies (WCF, WPF,...) but that is more of an attitude (it's still up to you to keep yourself up to date with more recent technologies).
All this aside, if you have to start today I would recomend to go for the most recent certification possible. So in your case, I'd go for the 4.0.
Dimitri C. - Please mark the replies as answers if they help! Thanks.