3rd gen 3rz, has 4 coil packs one for each cylinder. 2nd gen gens have 2 coil packs. 2 per cylinder. 1st gen have a distributor. They all have the same block so one is not easier then the other.
There is also a slight internal difference in the intake, and intake runners between 98 and 00 but that doesn't effect anything in the swap.
The other difference is the vacuum canisters. but if your not worried about emissions or a check engine light this also would make a difference to you.
3rd gens if i remember don't have an engine bay fuse box. Which can make things easier to swap. The key is get an manual!
