If you want to use 2 different versions of TurboTax for you and your spouse, then you will need to prepare your returns separately.

"Basic" is not available in TurboTax Online, it is only available in CD/Download form (for Windows).

Thank you,
If we file separately, is there any downside?

The downside is that the program can't see your spouse's information. You'll have to manually enter your wife's info, and she will have to enter yours. You'll also have to figure out yourself who claims things like donations, medical expenses, etc...