(0) Did the "too clean" explanation come from the dealer or the folks who actually make the decision? If you were turned down for credit reasons in the US, you are entitled to a copy of your credit report and a written explanation. Your credit report will say something about why your score is what it is.
(1) Your decision to buy an Element in three years should not affect what car you buy/lease today. If you were getting by with something smaller, why not stay smaller for now?
(2) I'd recheck the numbers. With a lease, you pay for estimated depreciation, which is quite significant over the first three years, with enough margin for the leasor to be wrong and still make a profit selling the car to someone else. I mention this because if you trade, you'll not only be paying the hybrid premium, you'll be restarting the depreciation clock.
You're planning to pay for at least $3k in depreciation and then pay the hybrid premium, which will probably be at least $3k.
If you're set on buying a hybrid in 3 years, buy a used car today. You'll pay less in interest on the loan and the depreciation should be less. You should be able to buy a car that will last three years for less than a new element will depreciate in that time.
Get a car for $2-3k and save the difference between those payments and your proposed lease payments for repairs and a bigger down payment in three years. And, if you can't save the difference, you just found out the easy way that you can't afford to buy a new hybrid. (A lot of Prius' will be coming off lease then.)