It is essentially 1 game so should they sell it as a single entity or should they sell them individually meaning you'd have to buy them separately?

EX: Monster Hunter 3rd (psp) + Monster Hunter 3rd Remastered (ps3)

Wipeout HD (ps3) + Wipeout HD (PSV)

Ruin (psv) + Ruin (ps3)

Should they? Yes.

Will they? No.

They should be bundled, the PS3 version should come with a token to download the PSP / PSV version for free.

They need to find a way to link them to eachother as well, say you can only use transfarring if both systems are logged into the same PSN account.

I think they should just bundle them so both sides will be somewhat happy. :)

The best scenario would be one where they would put them both in the same package for one price. The more likely, yet still quite unlikely, scenario would be the bundle one. It would need a serious discount though, maybe $10 more at most than the more expensive (PS3) version.

Buy one get the other for 90% off.

This.

Or at least have some discount code. Do they even still DO that? 

Yeah, at least a dicount code. Cuz, ya know, doesnt make sense you 2 games at full price.

Pretty much this in a nutshell. The best you can hope for is a discount on the other version via a voucher or something.