if you include cost of the engine, sure..

Gen3 offers more than just bolt ons, after you do all the bolt on mods to the gen2 you're STILL on a MAF based ECU which sucks and the only way around it while retaining worthy drivability is 1300$ worth of EMS parts vs the already map based gen3 which can be ran from the very affordable PowerFC

if you plan on replacing every part in the motor, I'd run gen2 also.. Only because parts are readily available at any dealer and since it was a usdm engine many American parts suppliers have it on their engine parts list.. But if I wanted a 350whp 3S I'd go gen3 all day and for more reasons than I've put