depends on the power you're looking for honestly
so if your goals are not ridiculously high the stock motor and tranny will be just fine
no reason to swap it
also the stock motor is almost worthless as far as selling..you'd typically get only a few hundred bucks for them..

also its not cheaper to swap it. why? you have to buy a 2jzgte $2000+ right there(thats for the cheaper auto swap)..then u have to pay to have it swapped...probably another $2000 or so depending on the place you take it too..unless you plan to do it yourself
then if u wanted a v160..another $3000+ for that tranny alone

if you wanted an xs power turbo kit for a NA-t setup..they are about $1800 then you need it installed plus some engine management...stock injectors/hg will do for a moderate 300-330whp which would be nice imo...

check out clubna-t.com and do some research there also.