In reply to edunn:
In what way is the data heteroskedastic?
It may be that linear regression isn't appropriate to your data so I'd plot the data (or the residuals) to check that linear regression really is the most appropriate method - that may also give you a clue as to how best to transform your data.
If the data is not badly heteroskedastic I wouldn't worry about it, but if it is then check your model isn't mis-specified - do you need to add any extra variables? Often heteroskedasticity is caused by subsets of the data being different for some reason (e.g. an unreliable group, problematic batch etc.)
If your residuals are heteroskedastic then you can't use R^2 as OLS doesn't minimize variance so comparing residual variance won't help. You could always try Generalized Least Squares regression (GLS). That will always give you BLUE estimates, but it's not a straightforward option.
Does it have to be one variable or the other?
If your two independent variables are not strongly correlated my approach would be to run
DV~IV1+IV2+IV2.IV2
Then do a stepwise regression using robust standard errors to get the best model - it's not a formal test but it will tell you what's most appropriate.