Arena is a really good way to get souls. I have every troop levelled, Dawnbringer and 2 million extra souls and I don’t own Pharos-Ra and I never soul farmed. I got all of that from normal battles with The Dragon Soul and Arena with Celestial Armor. The 2 million extra souls is mainly from Arena I stopped using Dragon Soul not long after I got Dawnbringer.
Because of the new daily quests the amount of gems are growing pretty fast. I am allready at about 650 gems. At the moment I use them only sometimes for the daily deals in the dungeon menue.
For what else should I keep or use them? Is it worth to buy 50 gem keys one time for 450 gems? So far I have drawn no legy minions, which are worth putting into my teams. 
For me, once you have the dragon armour and/or celestial armour (arguable if you need both this early on), the only thing worth spending gems on are gem, event or VIP keys. The idea, like people above have mentioned, is to get a few key legendary/mythic troops, or minions in your terminology. These troops are key to your continued progression in this game.
Some of these keys troops are:
Dragon soul
Krystenax
Khorvash
Infernus
Pharos ra
Ubastet
Etc
Once you have these keys troops, you can build more formidable teams with synergy and start conquering all before you.