Reproducing the Arena exactly as it was does not seem doable since that would require players actively building new decks, and most of the legacy etg community has its attention rightfully turned to Sparklmonkey's project.
Instead, here's my proposal:
1) Have a "Top50" that's actually a collection of notable fully upped PVP decks. They'd have 100HP and no bonus, so they'd be like a much harder AI3.
— Ideally this would include OTKs and other complex combos, but I assume that would require giving the AI specific instructions for each of those decks. I don't know if this is doable.
— This category is centred on PVP nostalgia, so it doesn't have to be a good way to farm. In fact it could just as well cost 0 to play and give no prize.
(— Also, I want that in regular oetg too :-p)
2) Also have a separate option for farming rares, where every deck is centered around some rare cards (with a focus on shards). Decks would have varying HP and bonuses to make the most of their strategy, for example SoBr and SoFre decks would focus on draw and mark power to maximize speed while SoDiv and SoFo decks would focus on HP and deck size to maximize endurance.
— Bonus rare spin after every N wins in a row, let's say 3.