You're not really paying to transport up, you're paying the sub for the Bank service, which at $5 a year isn't exactly expensive, it's a useful thing to have, loads of extra storage and it's going to be used for all gens going forward, as well as transferring Gen 1 from the VC games.
You can do a more convulated way of doing it using Pokegen and PKHex.
If you really don't want to pay for bank then you're going to need a way to back up your Gen 5 saves, if it's retail cart then either a save dongle or a DS console and DS homebrew running on a flash card and a slot 2 cartridge or find a guide for WiFi back up, either way you'll need a DS flash card and console, if you're running it on a flash card than just copy the save off. You're also going to need 3DS homebrew to back up your Gen 6 save.
Unless you have the things already to do it it would actually be cheaper to just buy a sub to bank.
Then you need to back up each Pokémon to a pkm file using pokegen, then use PKHex to import them all in to your Gen 6 save.