You could set up 2 separate legal entities, i.e. 2 ltd cos, 1 sole prop and 1 partnership, etc....
Provided both businesses were properly separate (separate accounts, bank accounts, invoices for any supplies between the two) then they would be separately registrable for VAT.
In theory, if either one or both were below the VAT registration threshold it need not register for VAT. However this would likely attract the attention of HM C&E who could issue a direction to treat the 2 businesses as one.
However, as you appear to wish to be registered for VAT, with both companies registered HM C&E are unlikely to be overly concerned about the separation.
This arrangement may have negative consequences for other taxes.
Regards
Paul Taylor
http://www.vatease.co.uk/