I agree that, for all things to be equal, the system has to be balanced out so that people using (for example) Flint, or Hoes, or Blaze Rods (etc) will be bound by the same effects, or - at the very least - have those weapons nerfed so that they will, in effect, be on-par with their Vanilla-Weapon counterparts.
On the old Map, I could spam-strike a player with a Diamond Axe, even if they were several times my superior, because there was no Attack Cooldown. While I enjoyed the power-trip (I only PvP in self-defense, so I got to feel all self-righteous and whatnot lol), abused en-masse by folks who like to misuse/abuse Plugin features (like a certain Cable Guy who will remain unnamed, and I don't mean Jim Carrey) could SEVERELY unbalance the game.
And, sheesh....if fights last longer, so what? Fights shouldn't be "Instant-gratification". They should be heated, intense, nerve-wracking, and require the utmost of your mental faculties. If every PvPer was chivalrous, refrained from Button-Mashing, and devised actual combat tactics (aside from "ooh, lets place bounties, but have our friends claim them, so they can place the next bounty" exploiter doofs), I wouldn't care whether the system changed or stayed the same.
But we're not dealing - with a few exceptions - with Tacticians, Chivalrous PvPers and people who think out and time their attacks. Most Minecraft PvPers are looking for a "quick fix" a le Button Mashing.
At least, that's been what I have personally observed, and experienced. You often know the types by how often their PKing flashes across the Server Broadcast system.