What unique role of Raikou not covered by zapdos?

I'm on the same boat with you, luckily got a 100iv Zapdos (most amazing part is I'm team instinct) and hv max it out.
Zapdos has better attack stat and more type resistance, it's only better moveset Raikou hv. And moveset may have a big chance to reroll after Gen 3 released (hopefully at Halloween). If Zapdos get equally good moveset than it's going to be the best electric attacker.

Thundershock/Wild Charge is incredible. Raikou with that moveset is strong enough to just be a generalist against anything that doesn't resist electric, and it shreds through anything that is weak to electric.

Charge Beam is the most annoying move in the game right now imo. Extremely slow, extremely low dps, and energy gain/sec is almost identical to Thundershock (13,64/13,33).
Raikou is the last one here (Europe), I'm not going to touch my Zapdos until movesets change (several +90%iv). If i need electric, i'd rather use Jolteons than Zapdos.

Edit: If we are able to use Legendaries as gym defenders someday, Charge Beam is superior to Thundershock. Dps is still bad, but the slow attack speed and high energy/hit is much better for gym defense. Also Zapdos typing is better than Raikou for defending imo.
So to answer your question, Zapdos makes a better gym defender than Raikou does.

Raikou does almost everything better. Except Solarbeam Ho-Oh, and a few other niches.

But Zapdos (and Jolteon too actually) could also learn TS/WC in Gen 6, so it could be added to Zapdos' movepool anytime.

Raikou is potentially a safer choice against a number of water types, many of which may have an Ice attack which is going to be SE versus Zapdos. Some with access to Rock moves as well, also SE, but you're probably going to be fighting most of those with Grass types.

Raikou beats Zapdos in any case

Zapdos is bad choice against water ice types like Lapras, and next in gen 3 Walrein, which against Raikou is better, against Ho-Oh Zap will shine more against SoB sets, aside of those matchups Raikou and Zapdos are almost the same, Raikou being better thanks to his movesets despite his lower attack

I have powered up a 96% iv Zapdos and I don't regret it. For me living in Europe Raikou is the last beast becoming available, so Zappy is a vialable option into Suicune for me, having just a Jolteon. When Raikou introduces after a month, I will have the resources to power up even Raikou, so having both is a good option if you want variety. Level 37 here, from Tirana Albania.