I would personally go with Groudon first since a SB Groudon is almost entirely separate from an EQ Groudon...could almost consider them two entirely different legendaries. Raikou would merely be a double. Having another one would certainly up your damage but I think unless raiders are incredibly sparse in your area you're better off with one Raikou behind a team of Jolteons and Exeggcutors.
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Multiple legendaries
So up until now the question wasn't really relevant for me to ask myself if I would power up multiple legendaries of one type. I was rather unlucky with Zapdos, Entei and Articuno. But now things have changed. With Raikou I got a 96% 13/15/15 and a 93% 14/15/13. I decided to power up the 93% one due to 14 attack. Now with Groudon I got a 100% on the first try and today caught a 15/14/15 98%. With gen3 being pretty underwhelming except for Metagross and the legendaries I think it would be pretty dumb to not go with the 98% one too and power him up. Having one with SoB and one EQ would be another benefit. Then there is raikou...he's by far the best counter to Kyrogue and a second one would up my damage by a lot. Would you go with those second ones in my situation even though I didn't want to power up multiple of one legend in the beginning? Rare candy are rare but not really a problem.
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Do you have a decent zapdos to power up instead of a second raikou ? Even tho raikou is better due to movesets in your position i wouldn't power up a second one (esp sense it has 13 atk) id use the dust and candy on either zapdos or that other Groudon...ps share that horseshoe with me a bit I have yet to get any Groudon over 93%
91% isn't that bad. I did about 30 Entei Raids and the best I've seen was 84%.
But you shouldn't hesitate to power up a Legendary which lacks good IVs. If my best Raikou had 10 attack I would power it up anyway. It's simply the best of its type and 1 or 2 less att IV are far away from changing that.
Right now a second Raikou is more efficient than a Raikou and a Zapdos. But if you prefer more diversity then go for the Zapdos.
